diff --git a/API.md b/API.md new file mode 100644 index 00000000..dd843774 --- /dev/null +++ b/API.md @@ -0,0 +1,502 @@ +# GET: /SessionInfo +Returns high-level configuration info on this VISION session. Mostly used +to enable/disable features in the visualizer. + +- 'name': A title for this session (shown in the top title bar) +- 'meta\_sigs': Names of meta-data signatures. Sent here as a convenience as +numeric meta-data signatures and gene signatures get combined in the display +and often lookups are needed to distinguish. +- 'ncells': Total number of cells +- 'pooled': Whether or not there is micro-pooling +- 'has\_sigs': Whether or not there are gene signatures +- 'has\_proteins': Whether or not there are CITE-seq proteins +- 'has\_lca': Whether or not LC Annotator analysis is available +- 'has\_tree': Whether or not Trajectories are available + +Response structure: +``` + { + 'name': 'Session Name', + 'meta_sigs': [list of string], + 'ncells': int, + 'pooled': bool, + 'has_sigs': bool, + 'has_proteins': bool, + 'has_lca': bool, + 'has_tree': bool, + } +``` + +# GET: /Signature/Scores/ +Return the per-cell signature scores for signature: `` +Data comes from obj@SigScores matrix + +Response structure: + +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number, per cell signature scores], + } +``` + +# GET: /Signature/Meta/ +Return the per-cell meta-data values for variable: `` +Data comes from obj@metaData dataframe + +Response structure: + +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number or string, per-cell meta-data values], + } +``` + +# GET: /Signature/Info/ +Returns information associated with a signature +Data comes from object@sigData + +Response structure: + +``` + { + 'sigDict': { # signature-gene weights + 'GeneName1': 1, + 'GeneName2': -1, + ... + }, + 'name': 'Signature Name', + 'source': 'Signature source', # typically filename where signature was loaded from + 'metaData': 'Signature description...', # second column in .gmt file + 'geneImportance': { # signature-gene importance values + 'GeneName1': .1, + 'GeneName2': .01, + ... + } + } +``` + +# GET: /Signature/Expression// +Returns expression values for `` grouped by ``. +This is used to generate the gene x cluster heatmap in the bottom left +Values are computed on the fly at the server + +Response structure +``` +{ + 'data': list of list of Number (2d matrix, outer index is row index) + 'sample_labels': column labels for the matrix in 'data' + 'gene_labels': row labels for the matrix in 'data' +} +``` + +# GET: /Proteins/\/Values +Returns the per-cell protein expression values for `` +Data comes from obj@proteinData matrix + +Response structure: +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number, per cell protein expression], + } +``` + +# GET: /FilterGroup/SigClusters/Normal +For each signature, describes the assignment of signatures to signature-clusters +This is used to group signatures in the upper-left section + +Response structure: +``` +{ + "Signature Name" (str): (int), + ... +} +``` + +# GET: /FilterGroup/SigClusters/Proteins +For each protein, describes the assignment of proteins to protein-clusters +Proteins aren't actually clustered in the interface. Every protein is assigned to cluster #1 + +Response structure: +``` +{ + "Protein Name" (str): 1, + ... +} +``` + +# GET: /FilterGroup/SigClusters/Meta +For each meta-data variable, describes the assignment of each variable to meta-data clusters +This is used when micropools are created to group factor variables with their expanded +percent-value-per-micropool representations + +Response structure: +``` +{ + "Metadata variable Name" (str): (int), + ... +} +``` + +# GET: /Projections//coordinates/ +Returns the coordinates for projection `` in column `` +Since the scatter plot can show more than just projects, this has been expanded to also +return coordinates from the latent space or other meta-data variables. `` can +come from names in object@Projections, or can be "Meta Data" to refer to object@metaData or +"Latent Space" to refer to object@LatentSpace. In either case `` should refer +to an associated column. + +Response structure: + +List of list of `[coordinate, 'cell id']` + +``` +[ + [coordinate (float): 'cell id' (str)], + [coordinate (float): 'cell id' (str)], + [coordinate (float): 'cell id' (str)], + ... +[ +``` + +# GET: /Projections/list +Returns information on projections and other variables that can be plotted in the main +scatter-plot panel. Used to create the dropdown menus. + +Response structure: + +Dictionary where keys are the name of projections/meta data/latent space and the values are +a list of the associated columns + +``` +{ + 'projection_name_1': list of column names in the projection, + 'projection_name_2': list of column names in the projection, + 'Meta Data': list of numeric meta-data variables, + 'Latent Space': list of column names in the latent space +} +``` + +# GET: /PearsonCorr/Normal +Gets information for the LC Annotator - the correlation of each signature with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N signatures x N components), + "pvals": list of list of p-values (N signatures x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of signature names in the same order as columns of 'zscores'/'pvals', +} +``` + +# GET: /PearsonCorr/Proteins +Gets information for the LC Annotator - the correlation of each protein with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N proteins x N components), + "pvals": list of list of p-values (N proteins x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of proteins names in the same order as columns of 'zscores'/'pvals', +} +``` + +# GET: /PearsonCorr/Meta +Gets information for the LC Annotator - the correlation of each numeric meta-data variable with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N variables x N components), + "pvals": list of list of p-values (N variables x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of variables names in the same order as columns of 'zscores'/'pvals', +} +``` + +# POST: /DE +Requests a differential expression analysis from the server. + +Determines the set of cells used for the numerator (i.e. _num or _n) and for the denominator (i.e. _denom or _d) + +Examples: +- To select cells in cluster 5 for the numerator set `'type_n': 'meta'`, `'subtype_n': 'cluster'`, `'group_num': 'Cluster 5'` +- To select cells in a saved manual selection for the numerator set `'type_n': 'saved_selection'`, `'group_num': 'name_of_selection'` +- To select a specific set of cell ids for the numerator set `'type_n': 'current'`, `'group_num': list of cell ids` + +Posted data structure: +``` +{ + 'type_n': either 'current', 'meta', or 'saved_selection' + 'type_d': either 'remainder', 'meta', or 'saved_selection' + 'subtype_n': which meta-data variable to group cells by if type_n is 'meta' + 'subtype_d': which meta-data variable to group cells by if type_d is 'meta' + 'group_num': list of cell ids (if type_n is 'current') OR name of saved selection (if type_n is 'saved_selection') + OR value of categorical meta-data variable (if type_n is 'meta') + 'group_denom': same behavior as 'group_num' + 'min_cells': (int) pre-filter genes expressed in less than this many cells + 'subsample_groups': (bool), whether or not to subsample each comparison group first + 'subsample_N': (int) size of the groups after subsampling. Ignored if 'subsample_groups' is false +} +``` + +Response structure: + +DE Results table with {'column name' -> list of values} + +``` +{ + 'Feature': list of feature (gene or protein) names + 'Type': list of either 'Gene' or 'Protein' + 'logFC': list of log-fold-change values + 'stat': list of AUC values + 'pval': list of FDR-corrected p-values +} +``` + + +# GET: /Clusters/MetaLevels +The display of the top-left area for signatures/proteins/meta-data depends on the selected +grouping variable in the dropdown. Commands scoped to a particular grouping variable are +nested under "/Clusters". + +This call returns a list of grouping variables and the levels/categories associated with them. + +Response structure: +``` + { + 'name of variable': [list of str - values this variable can take], + 'name of variable': [list of str - values this variable can take], + 'Cell Type': ['CD4+', 'CD8+', 'NK'], # For example + } +``` + +# GET: /Clusters//SigProjMatrix/Normal +Returns matrices consisting of test statistic and p-value for 1 vs. all differential signature +tests and for local autocorrelation. + +First column is "Score" and values are for local autocorrelation. Statistic is the 1 - Geary's C. + +Other columns are for 1 vs. all differential signature tests for each value in the selected grouping +variable in the dropdown. Test statistic are the AUC values from a ranksums test. P-values also +from this test. + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # signatures x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # signatures x cell group (+ 'Score') matrix of p-values + } +``` + +# GET: /Clusters//SigProjMatrix/Meta +Same as `/Clusters//SigProjMatrix/Normal`, but for meta-data variables + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # variables x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # variables x cell group (+ 'Score') matrix of p-values + } +``` +# GET: /Clusters//ProteinMatrix +Same as `/Clusters//SigProjMatrix/Normal`, but for CITE proteins + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # proteins x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # proteins x cell group (+ 'Score') matrix of p-values + } +``` + +# GET: /Clusters/list +Not used anymore + +# GET: /Clusters//Cells +Not used anymore + + +# GET: /Expression/Genes/List +Retrieves a list of genes for which expression values can be plotted. +Used to populate the dropdown in the 'Genes' tab. + +Response structure: +``` +[list of str - gene names] +``` +# GET: /Expression/Gene/ +Gets the per-cell expression of the gene specified by ``. +Expression values returned are on a log2 scale. + +Response structure: +Items in 'values' correspond to the cells in 'cells' in order +``` + { + 'cells': [list of str - cell identifiers], + 'values': [list of number - gene expression values], + } +``` + +# GET: /Cell//Meta +Retrieves meta-data information for an individual cell specified by `` + +Response structure: +``` + { + 'variable name': value (str or number), + 'variable name': value (str or number), + 'variable name': value (str or number), + ... + } +``` + +# POST: /Cells/Meta +Retrieves meta-data information for a group of cells + +Posted data structure +``` +[list of cell id] +``` + +Response structure: +``` + { + 'numeric': { + '': { + 'Min': , + 'Median': , + 'Max': , + }, + '': { + 'Min': , + 'Median': , + 'Max': , + }, + # Repeat for additional numeric meta-data variables + }, + 'factor': { + '': { + '': number (proportion of cells assigned to this level, + '': number (proportion of cells assigned to this level, + '': number (proportion of cells assigned to this level, + ... + } + # Repeat for additional factor meta-data variables + } + } +``` + +# GET: /Cells/Selections +Used when loading a selection of cells. + +Response structure: +``` +[list of str - names of saved selections] +``` + +# GET: /Cells/Selections/ +Retrieves the cells associated with the selection, `` + +Response structure: +``` +[list of str - cell ids in the indicated cell selection] +``` +# POST: /Cells/Selections/ +Saves a cell selection with name `` + +``` +[list of str - cell ids to be assigned to this cell selection] +``` + +# GET: /Tree/Projections/list +Get the list of different tree layouts that are available +Used to populate the 'Projection' dropdown under the 'Trajectories' view + +R version: returns the names of object@TrajectoryProjections + +Response structure: +``` +[list of str - names of tree projections] +``` + +# GET: /Tree/Projections//coordinates +Returns the coordinates for the tree layout `` in addition +to the position of individual cells + +Response structure: +``` + [ + [ + [, , ], # coordinates for individual cells + [, , ], + [, , ], + ... + ], + [ + [, ], # coordinates for internal tree nodes + [, ], + [, ], + ... + ], + [list of list of number] # 0/1 adjacency matrix for internal tree nodes + ] +``` + + +# GET: /Tree/SigProjMatrix/Normal +Returns matrices consisting of test statistic and p-value trajectory autocorrelation +Format is similar to `/Clusters//SigProjMatrix/Normal`, but without +the 1 vs all test results. + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # signatures x 1 matrix of test statistics + 'pvals': [list of list of number] # signatures x 1 matrix of p-values + } +``` + +# GET: /Tree/SigProjMatrix/Meta +Same as `/Tree/SigProjMatrix/Normal` but for meta-data variables + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # variables x 1 matrix of test statistics + 'pvals': [list of list of number] # variables x 1 matrix of p-values + } +``` + +# GET: /Tree/ProteinMatrix +Same as `/Tree/SigProjMatrix/Normal` but for CITE protein expression values + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # proteins x 1 matrix of test statistics + 'pvals': [list of list of number] # proteins x 1 matrix of p-values + } +``` diff --git a/DESCRIPTION b/DESCRIPTION index b5731929..88026868 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,17 @@ Package: VISION Title: Functional interpretation of single cell RNA-seq latent manifolds -Version: 2.1.0 +Version: 3.0.0 Authors@R: c(person("Matt", "Jones", email = "mattjones315@gmail.com", role = c("aut", "cre")), person("David", "Detomaso", email = "david.detomaso@berkeley.edu", role = c("aut", "cre")), person("Tal", "Ashuach", email = "tal_ashuach@berkeley.edu", role = c("aut")), + person("Yanay", "Rosen", email = "yanayrosen@berkeley.edu", role = c("aut")), person("Nir", "Yosef", email = "niryosef@berkeley.edu", role = c("ctb", "cph"))) Author: Matt Jones [aut, cre], David Detomaso [aut, cre], Tal Ashuach [aut], Nir Yosef [ctb] Maintainer: Matt Jones Description: VISION provides functional interpretation of single cell RNA-seq (scRNA-seq) latent manifolds through the use of biological signatures (which can be downloaded from online databases). VISION can operate downstream of other common analyses such as dimensionality reduction, clustering, or trajectory analysis of scRNA-seq data. VISION produces an interactive web-based output report that can be easily shared with other collaborators or the greater scientific community. Depends: R (>= 3.4) Imports: + dplyr, fastICA, igraph, irlba, @@ -40,7 +42,7 @@ Encoding: UTF-8 LazyData: true URL: https://yoseflab.github.io/VISION, https://github.com/yoseflab/VISION BugReports: https://github.com/YosefLab/VISION/issues -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Suggests: Biobase, BiocStyle, diff --git a/NAMESPACE b/NAMESPACE index 3eddf38e..0f3f698f 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,19 +1,37 @@ # Generated by roxygen2: do not edit by hand +export(PhyloVision) export(Vision) +export(addHotspotToVision) export(addSignatures) export(addTSNE) export(addUMAP) +export(analyzeHotspotObjectVision) export(analyzeLocalCorrelations) export(analyzeLocalCorrelationsModules) export(annotateLatentComponents) export(applyMicroClustering) export(calcModuleScores) export(calcSignatureScores) +export(calc_mod_sig_enrichment) +export(calc_set_enrichment) +export(clusterModScores) export(clusterSigScores) export(computeLatentSpace) export(convertGeneIds) export(createGeneSignature) +export(depthBasedCladewiseTreeCluster) +export(depthBasedTreeCluster) +export(draw_hotspot_heatmap) +export(generateOverlapSignatures) +export(group_modules_enrichment) +export(hsCalculateModuleScores) +export(hsComputeAutoCorrelations) +export(hsComputeLocalCorrelations) +export(hsCreateKnnGraph) +export(hsInit) +export(lca_based_depth) +export(loadHotspotObject) export(poolMatrixCols) export(poolMatrixRows) export(poolMetaData) @@ -21,6 +39,11 @@ export(read_10x) export(read_10x_h5) export(read_10x_h5_v2) export(read_10x_h5_v3) +export(runHotspot) +export(saveHSBytestToPickle) +export(treeClusterMinCladeSize) +export(trivial_dist) +exportMethods(PhyloVision) exportMethods(Vision) exportMethods(addProjection) exportMethods(analyze) @@ -33,6 +56,7 @@ exportMethods(getSelections) exportMethods(getSignatureAutocorrelation) exportMethods(getSignatureDifferential) exportMethods(getSignatureScores) +exportMethods(phyloAnalyze) exportMethods(saveAndViewResults) exportMethods(viewResults) import(Matrix) diff --git a/NEWS.md b/NEWS.md index fc8b5f31..7ada7135 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,14 @@ +# VISION 3.0.0 + +Major version bump! + +* Added support for Phylogenies as latent spaces in core VISION and integrated with VISION api +* Re-engineered UI into Signature Autocorrelation and Hotspot views +* Integrated [Hotspot](https://yoseflab.github.io/Hotspot/index.html) into VISION analysis and report UI. +* Deprecated support for trajectories and LC Annotator. +* New color-scheme for gene expression values + + # VISION 2.1.0 Added parameter `sig_gene_threshold` with **changed default behavior** diff --git a/R/AllClasses.R b/R/AllClasses.R index 11f87891..935cd28b 100644 --- a/R/AllClasses.R +++ b/R/AllClasses.R @@ -10,6 +10,8 @@ setClassUnion("numericORNULL", members = c("numeric", "NULL")) setClassUnion("matrixORSparse", members = c("matrix", "dgCMatrix")) setClassUnion("matrixORNULL", members = c("matrix", "NULL")) setClassUnion("dataframeORNULL", members = c("data.frame", "NULL")) +setClassUnion("rawORNULL", members = c("raw", "NULL")) + # setClassUnion("treeorNull", members=c("phylo", "NULL")) # setClassUnion("pythonorNull", members = c("python.builtin.object", "NULL")) @@ -121,7 +123,7 @@ Vision <- setClass("Vision", Pools = "list", LatentSpace = "matrix", LatentTrajectory = "trajectoryORNULL", - Hotspot = "list", + Hotspot = "rawORNULL", ModuleSignatureEnrichment = "list", ModuleHotspotScores = "data.frame", Viewer = "list", @@ -148,7 +150,7 @@ Vision <- setClass("Vision", Pools = list(), LatentSpace = matrix(NA, 1, 1), LatentTrajectory = NULL, - Hotspot = list(), + Hotspot = NULL, ModuleSignatureEnrichment = list(), ModuleHotspotScores = data.frame(), Viewer = list(), diff --git a/R/AllGenerics.R b/R/AllGenerics.R index b76e8a82..69d7e677 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -4,6 +4,8 @@ setGeneric("Vision", function(data, ...) { standardGeneric("Vision") }) +#' @rdname PhyloVision-class +#' @export setGeneric("PhyloVision", function(tree, ...) { standardGeneric("PhyloVision") }) diff --git a/R/AnalysisFunctions.R b/R/AnalysisFunctions.R index d272dee9..bc8a7a67 100644 --- a/R/AnalysisFunctions.R +++ b/R/AnalysisFunctions.R @@ -18,7 +18,7 @@ clusterCells <- function(object, tree=FALSE) { } else { message("Using Tree to compute clusters...\n") # Get the MRCA matrix and convert the node indexes to depths - cl <- treeCluster3(object@tree) + cl <- maxSizeCladewiseTreeCluster(object@tree) } names(cl) <- paste('Cluster', seq(length(cl))) diff --git a/R/Microclusters.R b/R/Microclusters.R index afb0459a..f7d0870e 100644 --- a/R/Microclusters.R +++ b/R/Microclusters.R @@ -326,6 +326,7 @@ readjust_clusters <- function(clusters, data, cellsPerPartition=100) { return(clusters) } + #' Pools columns of a numeric matrix #' #' Uses the provided pools to merge columns of the supplied data matrix @@ -383,6 +384,7 @@ poolMatrixRows <- function(data, pools) { return(pooled_data) } + #' create "super-cells" by pooling together single cells #' @param expr expression data (genes x cells matrix) #' @param pools cluster association of each cell @@ -418,13 +420,15 @@ poolMatrixCols_Inner <- function(expr, pools) { #' Performs a binary search on a depth d such that -#' if depth(u, v) <= d then u and v are in the same cluster +#' if depth(LCA(u, v)) <= d then u and v are in the same cluster #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate +#' @param target number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. -treeCluster <- function(tree, reach=10) { +#' +#' @export +depthBasedTreeCluster <- function(tree, target=10) { high <- length(tree$tip.label) low <- 0 while (T) { @@ -453,12 +457,12 @@ treeCluster <- function(tree, reach=10) { } } - if (num_clusters >= reach) { + if (num_clusters >= target) { if(low == d) { break } low <- d - } else if (num_clusters < reach) { + } else if (num_clusters < target) { if(high == d) { break } @@ -470,15 +474,17 @@ treeCluster <- function(tree, reach=10) { } -#' Performs a breadth first search to create a specific number of clusters -#' Clusters are split based on depth +#' Performs a breadth first search to create a specific number of clusters. +#' Clusters are split based on depth. #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate +#' @param target number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. -treeCluster2 <- function(tree, reach=10) { - if (reach > length(tree$tip.label)) { +#' +#' @export +depthBasedCladewiseTreeCluster <- function(tree, target=10) { + if (target > length(tree$tip.label)) { stop("Number of clusters is too high.") } @@ -498,7 +504,7 @@ treeCluster2 <- function(tree, reach=10) { cluster_parents[[as.name(child)]] <- node_depths[child] } - if (length(cluster_parents) >= reach) { + if (length(cluster_parents) >= target) { break } } @@ -515,19 +521,18 @@ treeCluster2 <- function(tree, reach=10) { } -#' Performs a bread first search to create a specific number of clusters -#' Clusters are split to prioritize cluster size +#' Performs a breadth first search to create a specific number of clusters +#' Clusters are split to prioritize max cluster size #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate -#' @return List of clusters, each entry being a vector of indices representing +#' @param target number of clusters to attempt to generate +#' @return List of clusters, each entry being a vector of tips representing #' samples in the cluster. -treeCluster3 <- function(tree, reach=10) { - if (reach > length(tree$tip.label)) { +maxSizeCladewiseTreeCluster <- function(tree, target=10) { + if (target > length(tree$tip.label)) { stop("Number of clusters is too high.") } - # node_depths <- node.depth(tree) root <- find_root(tree) cluster_parents <- c() cluster_parents[[as.name(root)]] <- get_max_cluster_size(tree, root) @@ -548,7 +553,6 @@ treeCluster3 <- function(tree, reach=10) { } } - cl <- list() for (cluster in seq_len(length(cluster_parents))) { cellId <- as.integer(names(cluster_parents)[cluster]) @@ -557,25 +561,71 @@ treeCluster3 <- function(tree, reach=10) { cl[[cluster]] <- all_children } - while (length(cl) > reach) { - cs <- c() - for (c in cl) { - cs <- append(cs, length(c)) - } - - smallest_i <- which.min(cs) - tip1 <- which(tree$tip.label == cl[[smallest_i]][1]) - dists <- c() - for (i in 1:length(cl)) { - tip2 <- which(tree$tip.label == cl[[i]][1]) - dists <- append(dists, trivial_dist(tree, tip1, tip2)) - } - - dists[smallest_i] <- dists[smallest_i] + max(dists) - closest_cluster_i <- which.min(dists) - cl[[min(c(closest_cluster_i, smallest_i))]] <- append(cl[[smallest_i]], cl[[closest_cluster_i]]) - cl[[max(c(closest_cluster_i, smallest_i))]] <- NULL + while (length(cl) > target) { + cs <- c() + for (c in cl) { + cs <- append(cs, length(c)) + } + + smallest_i <- which.min(cs) + tip1 <- which(tree$tip.label == cl[[smallest_i]][1]) + dists <- c() + for (i in 1:length(cl)) { + tip2 <- which(tree$tip.label == cl[[i]][1]) + dists <- append(dists, trivial_dist(tree, tip1, tip2)) + } + + dists[smallest_i] <- dists[smallest_i] + max(dists) + closest_cluster_i <- which.min(dists) + cl[[min(c(closest_cluster_i, smallest_i))]] <- append(cl[[smallest_i]], cl[[closest_cluster_i]]) + cl[[max(c(closest_cluster_i, smallest_i))]] <- NULL } return(cl) } + + +#' Generate clade-clusters for a tree of minimum size (unless children of root) +#' +#' +#' @param tree object of class phylo +#' @param minSize minimum clade size for a clade to be expanded +#' @return List of clusters, each entry being a vector of tips representing +#' WARNING: This won't work well for tree's with broad multifurcations +#' @export +treeClusterMinCladeSize <- function(tree, minSize=30) { + nodeLabels <- tree$node.label + numC <- length(tree$tip.label) + + # split into clusters for each one + cl <- list() + seen <- c() + i <- 1 # current cluster number + # sort groups by min cluster_size first + root <- find_root(tree) + queue <- c(root) + while (TRUE) { + # BFS on internal nodes + if (length(queue) < 1) { + break + } + internalNode <- queue[1] + queue <- queue[-1] + + + children <- get_children(tree, internalNode) + for (child in children) { + childMinSize <- get_min_cluster_size(tree, child) + if (childMinSize >= minSize){ + # continue expanding this child + queue <- append(queue, child) + } else { + # make this child a cluster + cl[[i]] <- get_all_children(tree, child) %>% (function(x) {return(tree$tip.label[x])}) + i <- i + 1 + } + } + + } + return(cl) +} \ No newline at end of file diff --git a/R/Projections.R b/R/Projections.R index 14b3316a..43f8e525 100644 --- a/R/Projections.R +++ b/R/Projections.R @@ -378,20 +378,28 @@ setMethod("computeKNNWeights", signature(object = "matrix"), ) -#' compute for each vector the weights to apply to it's K nearest neighbors +#' Compute for each vector the weights to apply to it's K nearest neighbors +#' #' @importFrom Matrix rowSums #' @importFrom Matrix sparseMatrix #' @importFrom matrixStats rowMaxs #' @param object tree to use for KNN #' @param K Number of neighbors to consider. +#' @param lcaKNN whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). +#' WARNING: lcaKNN doesn't perform well with broad multifurcations #' @return a list of two items: #' indices: matrix, cells X neighbors #' Each row specifies indices of nearest neighbors #' weights: matrix, cells X neighbors #' Corresponding weights to nearest neighbors setMethod("computeKNNWeights", signature(object = "phylo"), - function(object, K = round(sqrt(length(object$tip.label)))) { - k <- find_knn_parallel_tree(object, K) + function(object, K = round(sqrt(length(object$tip.label))), lcaKNN=FALSE, minSize=20) { + if (lcaKNN) { + k <- lcaBasedTreeKNN(object, minSize = minSize) + } else { + k <- find_knn_parallel_tree(object, K) + } + nn <- k[[1]] d <- k[[2]] diff --git a/R/Utilities.R b/R/Utilities.R index 99bc5840..598ed805 100644 --- a/R/Utilities.R +++ b/R/Utilities.R @@ -245,7 +245,7 @@ matrix_wilcox <- function(ranks, cluster_ii, #' @return pval - numeric vector, pvalue for each row #' @return stat - numeric vector, test statistic (AUC) for each row matrix_wilcox_cpp <- function(data, cluster_num, cluster_denom, - jobs = getOption("mc.cores", 2L)) { + jobs = getOption("mc.cores", 1L)) { # Subsetting individual rows is bad with a sparse matrix # instead we subset chunks at a time @@ -806,7 +806,6 @@ knn_tree <- function(leaves, k, distances) { } - #' Parallel KNN for Trees #' #' Computes nearest-neighbor indices and distances @@ -852,6 +851,46 @@ find_knn_parallel_tree <- function(tree, K) { return(list(index=idx, dist=dists)) } + + +#' Generate neighbors and weights for a tree object, based on LCA. +#' +#' @param tree object of class phylo +#' @param minSize the minimum number of neighbors per node +#' @return the hotspot object +lcaBasedTreeKNN <- function(tree, minSize=20) { + tips <- tree$tip.label + nTips <- length(tips) + neighbors <- data.frame(t(matrix(seq_len(nTips), ncol = nTips, nrow= nTips))) + rownames(neighbors) <- tips + + + weights <- data.frame(matrix(0, ncol = nTips, nrow= nTips)) + for (tip in seq_len(nTips)) { + my_neighbors <- minSizeCladeNeighbors(tree, tip, minSize) + + weights[tip, my_neighbors] <- 1 + } + + neighbors_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + weights_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + + for (tip in seq_len(nTips)) { + neighbors_no_diag[tip, ] <- neighbors[tip, -tip] + weights_no_diag[tip, ] <- weights[tip, -tip] + } + + rownames(neighbors_no_diag) <- tips + rownames(weights_no_diag) <- tips + + colnames(neighbors_no_diag) <- seq_len(nTips-1) - 1 + colnames(weights_no_diag) <- seq_len(nTips-1) - 1 + return(list("neighbors"=as.matrix(neighbors_no_diag), "weights"=as.matrix(weights_no_diag))) +} + + + + #' Generate an ultrametric tree #' #' @param tree an object of class phylo @@ -910,6 +949,40 @@ get_children <- function(tree, node) { return(children) } +#' Get the parent of a node +#' @param tree an object of class phylo +#' @param node the node to get parent +#' +#' @return the immediate parent of the mode, or the node if it is root +get_parent <- function(tree, node) { + edges <- tree$edge + parent <- edges[, 1][edges[, 2] == node] + if (length(parent) > 0){ + return(parent) + } + return(node) +} + + +#' Get's the nearest >= min size neighbors of a node based on clade structure +#' @param tree an object of class phylo +#' @param tip the tip to find the neighbors of +#' @param minSize the minimum number of neighbors of the node (excludes self) +#' +#' @return the neighbors +minSizeCladeNeighbors <- function(tree, tip, minSize=20) { + node <- tip + while (T) { + neighbors <- get_all_children(tree, node) + clade_size <- length(neighbors) + if (clade_size > minSize) { + return(neighbors) + } else { + node <- get_parent(tree, node) + } + } +} + #' Check if a child is a tip #' #' @param tree an object of class phylo @@ -948,7 +1021,10 @@ get_all_children <- function(tree, node) { return(tips) } - +#' Tree method for getting the max child clade size of a node +#' @param tree an object of class phylo +#' @param node the node to check +#' @return the size of the largest child clade get_max_cluster_size <- function(tree, node) { children <- get_children(tree, node) num_children <- c() @@ -959,32 +1035,90 @@ get_max_cluster_size <- function(tree, node) { } +#' Tree method for getting the min child clade size of a node +#' @param tree an object of class phylo +#' @param node the node to check +#' @return the size of the smallest child clade +get_min_cluster_size <- function(tree, node) { + children <- get_children(tree, node) + num_children <- c() + for (child in children) { + num_children <- append(num_children, length(get_all_children(tree, child))) + } + return(min(num_children)) +} + + +#' Trivial distance function for arbitrary tree clustering +#' +#' Number of mutations along path from tip1 to LCA(tip1, tip2) +#' Ensures if on same clade, join. +#' +#' @param tree an object of class phylo +#' @param tip1 the first leaf +#' @param tip2 the second leaf +#' @return the trivial distance between tip1, tip2 +#' +#' @export trivial_dist <- function(tree, tip1, tip2) { - depths <- node.depth(tree) - edges <- tree$edge - path1 <- c(tip1) - root <- find_root(tree) - parent <- tip1 - while (T) { - parent <- edges[, 1][edges[, 2] == parent] - path1 <- append(path1, parent) - if (parent == root) { - break - } + # node depths of tree + edges <- tree$edge + # Get the path from tip1 to root + path1 <- c(tip1) + root <- find_root(tree) + parent <- tip1 + while (T) { + parent <- edges[, 1][edges[, 2] == parent] + path1 <- append(path1, parent) + if (parent == root) { + break } - - path2 <- c(tip2) - parent <- tip2 - while (T) { - parent <- edges[, 1][edges[, 2] == parent] - path2 <- append(path2, parent) - if (parent == root || parent %in% path1) { - break - } + } + + mrca <- getMRCA(tree, c(tip1, tip2)) # MRCA of both + + + # Depths of the internal nodes that represent the parents of tip1, tip2 right before LCA + # ie the 'diverging' point or first split + path_length <- which(path1 == mrca) + + # Return the absolute difference between the depths + return(path_length) +} + + + + + +#' Depth of tip1 parent immediately after LCA(tip1, tip2) +#' +#' @param tree an object of class phylo +#' @param tip1 the first leaf +#' @param tip2 the second leaf +#' @return the trivial distance between tip1, tip2 +#' +#' @export +lca_based_depth <- function(tree, tip1, tip2) { + depths <- node.depth(tree) + edges <- tree$edge + # Get the path from tip1 to root + path1 <- c(tip1) + root <- find_root(tree) + parent <- tip1 + while (T) { + parent <- edges[, 1][edges[, 2] == parent] + path1 <- append(path1, parent) + if (parent == root) { + break } - - tip1_depth_prev <- depths[path1[which(path1 == path2[length(path2)]) - 1]] - tip2_depth_prev <- depths[path2[length(path2)] - 1] - - return(abs(tip1_depth_prev - tip2_depth_prev)) + } + + mrca <- getMRCA(tree, c(tip1, tip2)) # MRCA of both + + # Depths of the internal nodes that represent the parents of tip1, tip2 right before LCA + # ie the 'diverging' point or first split + lca_child_depth <- depths[path1[which(path1 == mrca) - 1]] + + # Return the absolute difference between the depths + return(lca_child_depth) } \ No newline at end of file diff --git a/R/methods-Module.R b/R/methods-Module.R index 114c77c3..34cf6ffe 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -1,88 +1,220 @@ +#' Perform Hotspot analysis on Vision Object +#' +#' @param object Vision Object +#' @param model model argument for Hotspot, one of \itemize{ +#' \item normal +#' \item danb +#' \item bernoulli +#' \item none +#' } +#' @param tree whether to use tree as latent space. If TRUE, object should have +#' a tree slot. +#' @param number_top_genes Hotspot argument for number of genes to consider +#' @param num_umi optional dataframe containing umi counts in first column for +#' barcodes +#' @param min_gene_threshold minimum number of genes in Hotspot module +#' @param n_neighbors number of neighbors to consider in latent space +#' @param autocorrelation_fdr threshold for significance for genes autocorr +#' @param clustering_fdr threshold for significance for clustering modules +#' @param logdata boolean, log the expression data, avoid for danb +#' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +#' and HotspotObject slots of object, as well as recalculates signature scores +#' for new modules. +#' @return the modified Vision object +#' +#' @export +runHotspot <- function(object, model="normal", tree=FALSE, + number_top_genes=1000, num_umi=NULL, + min_gene_threshold=20, n_neighbors=NULL, + autocorrelation_fdr=0.05, clustering_fdr=0.5, logdata=FALSE) { + + # Init Hotspot + hs <- hsInit(object, model, tree, num_umi, logdata) + # Init Hotspot KNN + hs <- hsCreateKnnGraph(hs, object, n_neighbors=n_neighbors) + # perform Hotspot analysis and store results in R + hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=number_top_genes, autocorrelation_fdr=autocorrelation_fdr) + # Compute localcorr + hs <- hsComputeLocalCorrelations(hs, hs_genes) + # Calculate Hotspot Module Scores for informative genes + hs <- hsCalculateModuleScores(hs, min_gene_threshold, clustering_fdr) + # Cluster Hotspot modules and perform Vision based analysis on HS Modules and + object <- analyzeHotspotObjectVision(object, hs, tree) + + return(object) +} -calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_genes=1000, - num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, - fdr_threshold=0.05) { +#' Init Hotspot object from Vision Object +#' +#' @param object the Vision Object +#' @param model the model for Hotspot (ie "normal", "danb"...) +#' @param tree boolean, whether to use the tree as ls +#' @param num_umi df of barcodes x num_umi +#' @param logdata boolean, log the expression data, avoid for danb +#' +#' @return the Hotspot object +#' +#' @export +hsInit <- function(object, model="normal", tree=F, num_umi=NULL, logdata=FALSE) { + hotspot <- import("hotspot", convert=F) + + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + + if (!logdata) { + # Don't take the log + exprData = object@exprData + } else { + # take the log2 otherwise + exprData = matLog2(object@exprData) + } + + gene_subset <- object@params$latentSpace$projectionGenes + + if (any(is.na(gene_subset))) { + gene_subset <- applyFilters(exprData, + object@params$latentSpace$projectionGenesMethod, + object@params$latentSpace$threshold, 2) + } + + exprData = as.data.frame(as.matrix(exprData)[gene_subset,]) + + # remove genes that do not have any standard deviation + sds = apply(exprData, 1, sd) + exprData = exprData[which(sds > 0), ] + + # generate the Hotspot object in python, potentially using the tree + if (tree) { + message("Using Tree") + ete3 <- import("ete3", convert=F) + nwk <- write.tree(object@tree) + pyTree <- ete3$Tree(nwk, format = 8L) + if (is.null(num_umi)) { + hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model) + } else { + py$umi_df <- r_to_py(num_umi) + py_run_string("umi_counts = umi_df.iloc[:, 0]") + hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model, umi_counts=py$umi_counts) + } + + } else { + if (is.null(num_umi)) { + hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model) + } else { + py$umi_df <- r_to_py(num_umi) + py_run_string("umi_counts = umi_df.iloc[:, 0]") + hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model, umi_counts=py$umi_counts) + } + } + + return(hs) +} - hotspot <- import("hotspot", convert=F) - workers <- getOption("mc.cores") - if (is.null(workers)){ - workers <- 1 - } +#' Init KNN graph in Hotspot object +#' +#' @return the Hotspot object with KNN initialized +#' +#' @export +hsCreateKnnGraph <- function(hs, object, n_neighbors=NULL) { + # create knn graph, specify nn or use object default + if (is.null(n_neighbors)) { + hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) + } else { + hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) + } + return(hs) +} - exprData = matLog2(object@exprData) - gene_subset = object@params$latentSpace$projectionGenes +#' Compute Hotspot auto correlations +#' +#' @param hs the Hotspot object +#' @param number_top_genes Hotspot argument for number of genes to consider +#' @param autocorrelation_fdr threshold for significance for genes autocorr +#' @return list of HS genes +#' +#' @export +hsComputeAutoCorrelations <- function(hs, number_top_genes=1000, autocorrelation_fdr=0.05) { + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + + hs_results <- hs$compute_autocorrelations(jobs=as.integer(workers)) + hs_genes <- hs_results$loc[hs_results$FDR$le(autocorrelation_fdr)]$sort_values('Z', ascending=F)$head(as.integer(number_top_genes))$index + return(hs_genes) +} - if (is.null(gene_subset)) { - gene_subset <- applyFilters(exprData, - object@params$latentSpace$projectionGenesMethod, - object@params$latentSpace$threshold, 2) - } - exprData = as.data.frame(as.matrix(object@exprData)[gene_subset,]) +#' Interface function to compute local correlations for Hotspot +#' Warning: modifies the hs argument +#' @param hs the Hotspot object +#' @param hs_genes Hotspot genes +#' @return the populated hs object +#' +#' @export +hsComputeLocalCorrelations <- function(hs, hs_genes) { + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + hs$compute_local_correlations(hs_genes, jobs=as.integer(workers)) + return(hs) +} - # remove genes that do not have any standard deviation - sds = apply(exprData, 1, sd) - exprData = exprData[which(sds > 0), ] - # TODO add UMI support - if (tree) { - message("Using Tree") - ete3 <- import("ete3", convert=F) - nwk <- write.tree(object@tree) - pyTree <- ete3$Tree(nwk, format = 8L) - if (is.null(num_umi)) { - hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model) - } else { - py$umi_df <- r_to_py(num_umi) - py_run_string("umi_counts = umi_df.iloc[:, 0]") - hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model, umi_counts=py$umi_counts) - } - - } else { - if (is.null(num_umi)) { - hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model) - } else { - py$umi_df <- r_to_py(num_umi) - py_run_string("umi_counts = umi_df.iloc[:, 0]") - hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model, umi_counts=py$umi_counts) - } - } +#' Analyze a Hotspot object using built in methods such +#' such as local correlation, signature overlap, etc. +#' Necessary to run this function for Hotspot functionality in viewer to work. +#' +#' @param object the VISION object +#' @param hs the Hotspot python object loaded by Reticulate +#' @param tree whether to use tree as latent space. If TRUE, object should have a tree +#' +#' @return the modified VISION object with the following slots filled: +#' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +#' and HotspotObject slots of object, as well as recalculates signature scores +#' for new modules. +#' +#' @export +analyzeHotspotObjectVision <- function(object, hs, tree=FALSE) { + hs_module_scores <- hs$module_scores + hs_modules <- hs$modules - if (is.null(n_neighbors)) { - hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) - } else { - hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) + # handle annoying reticulate conversion issues when writing to a file + if (!is.data.frame(hs_module_scores)) { + hs_module_scores <- py_to_r(hs_module_scores) } - - hs_results <- hs$compute_autocorrelations(jobs=as.integer(workers)) - hs_genes <- hs_results$loc[hs_results$FDR$le(fdr_threshold)]$sort_values('Z', ascending=F)$head(as.integer(number_top_genes))$index - hs$compute_local_correlations(hs_genes, jobs=as.integer(workers)) - hs$create_modules(min_gene_threshold=as.integer(min_gene_threshold)) - hs_module_scores <- py_to_r(hs$calculate_module_scores()) - hs_modules <- py_to_r(hs$modules) + if (!is.array(hs_modules)) { + hs_modules <- py_to_r(hs_modules) + } modules <- list() + # add the modules with name scheme HOTSPOT_{TREE if using TREE}_# + model <- hs$model for (i in unique(c(hs_modules))) { if (i !=-1) { names <- dimnames(hs_modules[hs_modules == i])[[1]] v <- rep(1, length(names)) names(v) <- names if (tree) { - new_sig <- Signature(sigDict = v, name=paste("HOTSPOT_TREE", i, sep = "_"), source="Hotspot", meta=paste("Hotspot on tree, model:", model)) - modules[[paste("HOTSPOT_TREE", i, sep = "_")]] <- new_sig + new_sig <- Signature(sigDict = v, name=paste("HOTSPOT_TREE", i, sep = "_"), source="Hotspot", meta=paste("Hotspot on tree, model:", model)) + modules[[paste("HOTSPOT_TREE", i, sep = "_")]] <- new_sig } else { - new_sig <- Signature(sigDict = v, name=paste("HOTSPOT", i, sep = "_"), source="Hotspot", meta=paste("Hotspot, model:", model)) - modules[[paste("HOTSPOT", i, sep = "_")]] <- new_sig + new_sig <- Signature(sigDict = v, name=paste("HOTSPOT", i, sep = "_"), source="Hotspot", meta=paste("Hotspot, model:", model)) + modules[[paste("HOTSPOT", i, sep = "_")]] <- new_sig } } } - colnames(hs_module_scores) <- names(modules) + # store module scores + colnames(hs_module_scores) <- sort(names(modules)) object@modData <- modules if (length(object@sigData) > 0) { @@ -94,22 +226,62 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge # calculate overlap signatures object <- generateOverlapSignatures(object) - # normal analysis + # re run normal analysis object <- calcModuleScores(object) object <- clusterModScores(object) - object@Hotspot <- list(hs) + object@ModuleHotspotScores <- hs_module_scores object <- analyzeLocalCorrelationsModules(object, tree) - + # save the Hotspot object + object <- addHotspotToVision(object, hs) return(object) } +#' Create Hotspot Modules and calculate module scores given a HS object +#' with local correlations already calculated +#' +#' @param hs the Hotspot object, must have ran compute_local_correlations already +#' @param min_gene_threshold min genes per module +#' @param clustering_fdr p value for clustering genes +#' @return the modified hs object +#' +#' @export +hsCalculateModuleScores <- function(hs, min_gene_threshold=20, clustering_fdr=0.5, plot=F) { + hs$create_modules(min_gene_threshold=as.integer(min_gene_threshold), fdr_threshold=clustering_fdr) + hs$calculate_module_scores() + + if (plot) { + draw_hotspot_heatmap(hs) + } + + return(hs) +} + + +#' Add HS python obj to vision OBJECT +#' +#' @param object Vision object +#' @param hs python hs object +#' @return Vision object with hs populated +#' +#' @export +addHotspotToVision <- function(object, hs) { + # save the Hotspot object + pickle <- import("pickle", convert=F) + py$hs <- hs + py$pickle <- pickle + py_run_string("hs_byte_array = bytearray(pickle.dumps(hs))") + hs_pickled_r <- as.raw(py$hs_byte_array) + object@Hotspot <- hs_pickled_r + + return(object) +} -#' calculate module scores +#' Calculate module scores (signature scores but on the modules) #' #' For each module-cell pair, compute a score that captures the level of #' correspondence between the cell and the module. @@ -123,6 +295,7 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge #' the overall signature score. Default = TRUE. This is used for inspecting #' genes in a signature in the output report #' @return the VISION object, with the @ModScores and @ModGeneImportance slots populated +#' #' @export calcModuleScores <- function( object, mod_norm_method = NULL, mod_gene_importance = TRUE) { @@ -178,16 +351,17 @@ calcModuleScores <- function( } - - #' Compute local correlations for all modules #' #' This is the main analysis function. For each filtered dataset, a set of #' different projection onto low-dimensional space are computed, and the #' consistency of the resulting space with the signature scores is computed #' to find signals that are captured successfully by the projections. +#' #' @param object the VISION object +#' @param tree whether to use the tree object as latent space for neighbors #' @return the VISION object with values set for the analysis results +#' #' @export analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { @@ -230,13 +404,26 @@ analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { return(object) } -calc_mod_sig_enrichment <- function(object) { + +#' Computes the hypergeometric overlap test for modules and signatures +#' +#' @param object the Vision object. +#' @param skip_down whether to ignore down signatures in overlap +#' @return list(statistic values, p values, clusters of signatures) +#' +#' @export +calc_mod_sig_enrichment <- function(object, skip_down=TRUE) { modules <- object@modData original_signatures <- object@sigData signatures <- list() sig_names <- list() for (signature in original_signatures) { + # calculate enrichment for both the up signal and down signal signature genes directional <- all(c(1, -1) %in% signature@sigDict) + down_reg <- all(signature@sigDict == -1) + if (skip_down && down_reg) { + next + } if (directional) { up <- names(which(signature@sigDict == 1)) down <- names(which(signature@sigDict == -1)) @@ -245,10 +432,13 @@ calc_mod_sig_enrichment <- function(object) { down_name <- paste(signature@name, "_DOWN", sep = "") signatures <- c(signatures, list(up)) - signatures <- c(signatures, list(down)) - sig_names <- append(sig_names, up_name) - sig_names <- append(sig_names, down_name) + + if (!skip_down) { + signatures <- c(signatures, list(down)) + sig_names <- append(sig_names, down_name) + } + } else { signatures <- c(signatures, list(names(signature@sigDict))) sig_names <- append(sig_names, signature@name) @@ -257,6 +447,7 @@ calc_mod_sig_enrichment <- function(object) { genes <- rownames(object@exprData) + # calculate the enrichments stats <- c() p_values <- c() for (signature in signatures) { @@ -284,13 +475,23 @@ calc_mod_sig_enrichment <- function(object) { colnames(p_values) <- mod_names rownames(p_values) <- sig_names + # group the signatures assignments <- group_modules_enrichment(stats, p_values) return(list("statistics"=stats, "p_vals"=p_values, "cl"=assignments)) } - +#' Calculate the hypergeometric enrichment for two sets from a population +#' Statisic = log (observed overlap / expected overlap) +#' P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) +#' +#' @param set1 the first gene set +#' @param set2 the second gene set +#' @param genes the population +#' @return c(statistic, p value) +#' +#' @export calc_set_enrichment <- function(set1, set2, genes) { N <- length(genes) m <- max(length(set1), length(set2)) @@ -310,6 +511,15 @@ calc_set_enrichment <- function(set1, set2, genes) { } +#' Make the clusters for the modules by enrichment. +#' For now we just assign each signature to each cluster, could filter to only include once, +#' so that each one appears in the modules x sigs table. +#' +#' @param stats overlap stats from calc_set_enrichment +#' @param pvals overlap p values from calc_set_enrichment +#' @return assignments of each signature to each module +#' +#' @export group_modules_enrichment <- function(stats, pvals) { sigs <- rownames(stats) mods <- colnames(stats) @@ -321,6 +531,11 @@ group_modules_enrichment <- function(stats, pvals) { } +#' Generates signature objects for the overlap sets between modules and signatures +#' @param object the Vision object +#' @return Vision Object, populates the modData slot with overlap signatures. +#' +#' @export generateOverlapSignatures <- function(object) { message("Generating Module Signature Overlaps...\n") sigs <- rownames(object@ModuleSignatureEnrichment$statistics) @@ -348,8 +563,6 @@ generateOverlapSignatures <- function(object) { } - - #' Compute Ranksums Test, for all factor meta data. One level vs all others #' #' @importFrom pbmcapply pbmclapply @@ -358,6 +571,7 @@ generateOverlapSignatures <- function(object) { #' @param object the VISION object #' @param variables which columns of the meta-data to use for comparisons #' @return the VISION object with the @ClusterComparisons modules slot populated +#' #' @export clusterModScores <- function(object, variables = "All") { @@ -430,7 +644,121 @@ clusterModScores <- function(object, variables = "All") { object@ClusterComparisons[["Modules"]] <- out return(object) +} + + +#' Load in an existing Hotspot object from bytes or a file +#' +#' @param file optional path to an existing file containing pickled bytes (format 0) +#' @param bytes optional R character vector of bytes created by calcHotspotModules +#' @return an externalptr to a Hotspot Object loaded in the R reticulate session +#' +#' @export +loadHotspotObject <- function(file=NULL, bytes=NULL) { + hotspot <- import("hotspot", convert=F) + pickle <- import("pickle", convert=F) + py$pickle <- pickle + + if (!is.null(file)) { + # load file + hs <- py_load_object(file) + return(hs) + } else if (!is.null(bytes)) { + py$hs_bytes <- r_to_py(bytes) + py_run_string("hs = pickle.loads(hs_bytes)") + return(py$hs) + } else { + return(NULL) + } +} + + +#' Save bytes in the Hotspot object slot to a file +#' @param path the file path +#' @param bytes the raw bytes, like in the Hotspot slot of a VISION Object +#' +#' @export +saveHSBytestToPickle <- function(path, bytes) { + py_save_object(obj=loadHotspotObject(bytes=bytes), path) +} + + +#' Add custom tree based neighbor and weights to a Hotspot object +#' +#' @param tree object of class phylo +#' @param the Hotspot object to add the nw to +#' @param minSize the minimum number of neighbors of the node +#' @return the Hotspot object +#' +#' @export +lcaBasedHotspotNeighbors <- function(tree, hotspot, minSize=20) { + tips <- tree$tip.label + nTips <- length(tips) + neighbors <- data.frame(t(matrix(seq_len(nTips) -1, ncol = nTips, nrow= nTips))) + rownames(neighbors) <- tips + + weights <- data.frame(matrix(0, ncol = nTips, nrow= nTips)) + for (tip in seq_len(nTips)) { + my_neighbors <- minSizeCladeNeighbors(tree, tip, minSize) + + weights[tip, my_neighbors] <- 1 + } + + neighbors_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + weights_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + + for (tip in seq_len(nTips)) { + neighbors_no_diag[tip, ] <- neighbors[tip, -tip] + weights_no_diag[tip, ] <- weights[tip, -tip] + } + + rownames(neighbors_no_diag) <- tips + rownames(weights_no_diag) <- tips + + colnames(neighbors_no_diag) <- seq_len(nTips-1) - 1 + colnames(weights_no_diag) <- seq_len(nTips-1) - 1 + return(list("neighbors"=neighbors_no_diag, "weights"=weights_no_diag)) } +#' Draw Modules Heatmap (Gene x Gene) +#' +#' @param hs the Hotspot Object +#' @param palette palette +#' @export +draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm")) { + scipy_hierarchy <- import("scipy.cluster.hierarchy", convert=F) + np <- import("numpy") + linkage <- hs$linkage + py_dend = scipy_hierarchy$dendrogram(linkage) + lcz = hs$local_correlation_z + gene_order = colnames(lcz)[np$array(py_dend$leaves)+1] + col_mapping = c() + module_to_col = list() + hs$modules = as.character(hs$modules) + unique_mods = as.character(unique(hs$modules)) + example_genes = list() + col_mapping[["-1"]] = "#ffffff" + for (i in 1:length(unique_mods)) { + mod = unique_mods[[i]] + if (mod != -1) { + col_mapping[[mod]] = palette[[i]] + module_to_col[[mod]] = palette[[i]] + example_genes[[mod]] = sample(hs$modules[hs$modules == mod], 5) + } + } + + modules = data.frame("module" = hs$modules) + modules$module = as.character(modules$module) + ha = rowAnnotation(df = modules, + col = col_mapping, + simple_anno_size = unit(0.5, "in")) + ht = Heatmap(as.matrix(lcz), name = "mat", + show_row_names=F, show_column_names=F, show_row_dend=F, show_column_dend=F, + row_order = gene_order, column_order=gene_order, + right_annotation=ha, + column_names_gp = gpar(fontsize = c(1)), + width = unit(5, "in"), height = unit(5, "in")) + draw(ht) +} diff --git a/R/methods-Signature.R b/R/methods-Signature.R index 6943c4a5..309270c3 100644 --- a/R/methods-Signature.R +++ b/R/methods-Signature.R @@ -61,8 +61,6 @@ Signature <- function(sigDict, name, source, metaData="") { stop("Missing source file.") } - names(sigDict) <- toupper(names(sigDict)) - .Object <- new("Signature", sigDict = sigDict, name = name, source = source, metaData = metaData) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index 9082dd60..5d95d54e 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -90,7 +90,7 @@ setMethod("Vision", signature(data = "matrixORSparse"), "rank_norm_columns"), pool="auto", cellsPerPartition=10, name=NULL, num_neighbors = NULL, latentSpace = NULL, latentSpaceName = NULL, latentTrajectory = NULL, - tree = NULL, modData = list(), hotspot= list(), pools=list()) { + tree = NULL, modData = list(), hotspot= NULL, pools=list()) { .Object <- new("Vision") @@ -107,7 +107,6 @@ setMethod("Vision", signature(data = "matrixORSparse"), .Object@params$signatures <- list() .Object@params$micropooling <- list() - rownames(data) <- toupper(rownames(data)) toRemove <- rownames(data)[duplicated(rownames(data))] if (length(toRemove) > 0){ message(sprintf( @@ -120,7 +119,10 @@ setMethod("Vision", signature(data = "matrixORSparse"), } if (!is.null(tree)) { - data = data[,tree$tip.label] + # Subset matrix + data <- data[,tree$tip.label] + # Subset Tree + tree <- keep.tip(tree, colnames(data)) } .Object@exprData <- data @@ -139,7 +141,6 @@ setMethod("Vision", signature(data = "matrixORSparse"), } # unnormalizedData might have more genes than exprData # and it might have more cells than exprData - rownames(unnormalizedData) <- toupper(rownames(unnormalizedData)) HAS_CORRECT_CELLS <- length(setdiff( colnames(.Object@exprData), colnames(unnormalizedData) @@ -267,10 +268,8 @@ setMethod("Vision", signature(data = "matrixORSparse"), .Object@params$latentSpace$projectionGenesMethod <- projection_genes .Object@params$latentSpace$projectionGenes <- NA } else { - print("Here") .Object@params$latentSpace$projectionGenesMethod <- NA - .Object@params$latentSpace$projectionGenes <- vapply( - projection_genes, toupper, "", USE.NAMES = FALSE) + .Object@params$latentSpace$projectionGenes <- projection_genes .Object@params$latentSpace$projectionGenes = intersect(rownames(.Object@exprData), .Object@params$latentSpace$projectionGenes) } @@ -411,6 +410,13 @@ setMethod("Vision", signature(data = "matrixORSparse"), } ) + +#' Initializes a new PhyloVision Object +#' +#' @param tree parsed ape tree +#' @param ... arguments passed to the base Vision constructor +#' @rdname PhyloVision-class +#' @export setMethod("PhyloVision", signature(tree="phylo"), function(tree, ...) { obj <- Vision(...) @@ -726,7 +732,7 @@ setMethod("analyze", signature(object="Vision"), if (hotspot) { message("Hotspot Analysis") - object <- calcHotspotModules(object, model="danb", tree) + object <- runHotspot(object, model="danb", tree) } @@ -735,6 +741,12 @@ setMethod("analyze", signature(object="Vision"), return(object) }) + +#' Analyze a PhyloVision object +#' +#' @param ... arguments passed to the base Vision constructor +#' @aliases phyloAnalyze +#' @export setMethod("phyloAnalyze", signature(object="PhyloVision"), function(object, hotspot=FALSE) { object <- analyze(object, tree=TRUE, hotspot=hotspot) diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..945dddb6 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,194 @@ + + + + + + + + +Page not found (404) • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ + + +
+ + + +
+
+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/API.html b/docs/API.html new file mode 100644 index 00000000..6cd6af69 --- /dev/null +++ b/docs/API.html @@ -0,0 +1,634 @@ + + + + + + + + +GET: /SessionInfo • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

GET: /SessionInfo

+
+ + +
+ +

Returns high-level configuration info on this VISION session. Mostly used to enable/disable features in the visualizer.

+
    +
  • ‘name’: A title for this session (shown in the top title bar)
    • +
  • ‘meta_sigs’: Names of meta-data signatures. Sent here as a convenience as numeric meta-data signatures and gene signatures get combined in the display and often lookups are needed to distinguish.
    • +
  • ‘ncells’: Total number of cells
    • +
  • ‘pooled’: Whether or not there is micro-pooling
    • +
  • ‘has_sigs’: Whether or not there are gene signatures
    • +
  • ‘has_proteins’: Whether or not there are CITE-seq proteins
    • +
  • ‘has_lca’: Whether or not LC Annotator analysis is available
    • +
  • ‘has_tree’: Whether or not Trajectories are available
    • +
+

Response structure:

+
    {
+        'name': 'Session Name',
+        'meta_sigs': [list of string],
+        'ncells': int,
+        'pooled': bool,
+        'has_sigs': bool,
+        'has_proteins': bool,
+        'has_lca': bool,
+        'has_tree': bool,
+    }
+
+
+

+GET: /Signature/Scores/ +

+

Return the per-cell signature scores for signature: <sig_name> Data comes from matrix

+

Response structure:

+
    {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number, per cell signature scores],
+    }
+
+
+

+GET: /Signature/Meta/ +

+

Return the per-cell meta-data values for variable: <sig_name> Data comes from dataframe

+

Response structure:

+
    {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number or string, per-cell meta-data values],
+    }
+
+
+

+GET: /Signature/Info/ +

+

Returns information associated with a signature Data comes from

+

Response structure:

+
    {
+        'sigDict': { # signature-gene weights
+            'GeneName1': 1, 
+            'GeneName2': -1,
+            ...
+        },
+        'name': 'Signature Name',
+        'source': 'Signature source', # typically filename where signature was loaded from
+        'metaData': 'Signature description...', # second column in .gmt file
+        'geneImportance': { # signature-gene importance values
+            'GeneName1': .1,
+            'GeneName2': .01, 
+            ...
+        }
+    }
+
+
+

+GET: /Signature/Expression// +

+

Returns expression values for <sig_name> grouped by <cluster_var>. This is used to generate the gene x cluster heatmap in the bottom left Values are computed on the fly at the server

+

Response structure

+
{
+    'data': list of list of Number  (2d matrix, outer index is row index)
+    'sample_labels': column labels for the matrix in 'data'
+    'gene_labels': row labels for the matrix in 'data'
+}
+
+
+

+GET: /Proteins/<protein_name>/Values

+

Returns the per-cell protein expression values for <protein_name> Data comes from matrix

+

Response structure:

+
    {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number, per cell protein expression],
+    }
+
+
+

+GET: /FilterGroup/SigClusters/Normal

+

For each signature, describes the assignment of signatures to signature-clusters This is used to group signatures in the upper-left section

+

Response structure:

+
{
+    "Signature Name" (str): <cluster_number> (int),
+    ...
+}
+
+
+

+GET: /FilterGroup/SigClusters/Proteins

+

For each protein, describes the assignment of proteins to protein-clusters Proteins aren’t actually clustered in the interface. Every protein is assigned to cluster #1

+

Response structure:

+
{
+    "Protein Name" (str): 1,
+    ...
+}
+
+
+

+GET: /FilterGroup/SigClusters/Meta

+

For each meta-data variable, describes the assignment of each variable to meta-data clusters This is used when micropools are created to group factor variables with their expanded percent-value-per-micropool representations

+

Response structure:

+
{
+    "Metadata variable Name" (str): <cluster_number> (int),
+    ...
+}
+
+
+

+GET: /Projections//coordinates/ +

+

Returns the coordinates for projection <proj_name> in column <proj_col> Since the scatter plot can show more than just projects, this has been expanded to also return coordinates from the latent space or other meta-data variables. <proj_name> can come from names in , or can be “Meta Data” to refer to or “Latent Space” to refer to . In either case <proj_name> should refer to an associated column.

+

Response structure:

+

List of list of [coordinate, 'cell id']

+
[
+    [coordinate (float): 'cell id' (str)],
+    [coordinate (float): 'cell id' (str)],
+    [coordinate (float): 'cell id' (str)],
+    ...
+[
+
+
+

+GET: /Projections/list

+

Returns information on projections and other variables that can be plotted in the main scatter-plot panel. Used to create the dropdown menus.

+

Response structure:

+

Dictionary where keys are the name of projections/meta data/latent space and the values are a list of the associated columns

+
{
+    'projection_name_1': list of column names in the projection,
+    'projection_name_2': list of column names in the projection,
+    'Meta Data': list of numeric meta-data variables,
+    'Latent Space': list of column names in the latent space
+}
+
+
+

+GET: /PearsonCorr/Normal

+

Gets information for the LC Annotator - the correlation of each signature with each latent component

+

Response structure:

+
{
+    "zscores": list of list of correlation coefficients (N signatures x N components),
+    "pvals": list of list of p-values (N signatures x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of signature names in the same order as columns of 'zscores'/'pvals',
+}
+
+
+

+GET: /PearsonCorr/Proteins

+

Gets information for the LC Annotator - the correlation of each protein with each latent component

+

Response structure:

+
{
+    "zscores": list of list of correlation coefficients (N proteins x N components),
+    "pvals": list of list of p-values (N proteins x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of proteins names in the same order as columns of 'zscores'/'pvals',
+}
+
+
+

+GET: /PearsonCorr/Meta

+

Gets information for the LC Annotator - the correlation of each numeric meta-data variable with each latent component

+

Response structure:

+
{
+    "zscores": list of list of correlation coefficients (N variables x N components),
+    "pvals": list of list of p-values (N variables x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of variables names in the same order as columns of 'zscores'/'pvals',
+}
+
+
+

+POST: /DE

+

Requests a differential expression analysis from the server.

+

Determines the set of cells used for the numerator (i.e. _num or _n) and for the denominator (i.e. _denom or _d)

+

Examples:

+
    +
  • To select cells in cluster 5 for the numerator set 'type_n': 'meta', 'subtype_n': 'cluster', 'group_num': 'Cluster 5' +
    • +
  • To select cells in a saved manual selection for the numerator set 'type_n': 'saved_selection', 'group_num': 'name_of_selection' +
    • +
  • To select a specific set of cell ids for the numerator set 'type_n': 'current', 'group_num': list of cell ids +
    • +
+

Posted data structure:

+
{
+    'type_n': either 'current', 'meta', or 'saved_selection'
+    'type_d':  either 'remainder', 'meta', or 'saved_selection'
+    'subtype_n': which meta-data variable to group cells by if type_n is 'meta'
+    'subtype_d': which meta-data variable to group cells by if type_d is 'meta'
+    'group_num': list of cell ids (if type_n is 'current') OR name of saved selection (if type_n is 'saved_selection')
+                 OR value of categorical meta-data variable (if type_n is 'meta')
+    'group_denom': same behavior as 'group_num'
+    'min_cells': (int) pre-filter genes expressed in less than this many cells
+    'subsample_groups': (bool), whether or not to subsample each comparison group first
+    'subsample_N': (int) size of the groups after subsampling.  Ignored if 'subsample_groups' is false
+}
+

Response structure:

+

DE Results table with {‘column name’ -> list of values}

+
{
+    'Feature': list of feature (gene or protein) names
+    'Type': list of either 'Gene' or 'Protein' 
+    'logFC': list of log-fold-change values
+    'stat': list of AUC values
+    'pval': list of FDR-corrected p-values
+}
+
+
+

+GET: /Clusters/MetaLevels

+

The display of the top-left area for signatures/proteins/meta-data depends on the selected grouping variable in the dropdown. Commands scoped to a particular grouping variable are nested under “/Clusters”.

+

This call returns a list of grouping variables and the levels/categories associated with them.

+

Response structure:

+
    {
+        'name of variable': [list of str - values this variable can take],
+        'name of variable': [list of str - values this variable can take],
+        'Cell Type': ['CD4+', 'CD8+', 'NK'],   # For example
+    }
+
+
+

+GET: /Clusters//SigProjMatrix/Normal +

+

Returns matrices consisting of test statistic and p-value for 1 vs. all differential signature tests and for local autocorrelation.

+

First column is “Score” and values are for local autocorrelation. Statistic is the 1 - Geary’s C.

+

Other columns are for 1 vs. all differential signature tests for each value in the selected grouping variable in the dropdown. Test statistic are the AUC values from a ranksums test. P-values also from this test.

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # signatures x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # signatures x cell group (+ 'Score') matrix of p-values
+    }
+
+
+

+GET: /Clusters//SigProjMatrix/Meta +

+

Same as /Clusters/<cluster_variable>/SigProjMatrix/Normal, but for meta-data variables

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # variables x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # variables x cell group (+ 'Score') matrix of p-values
+    }
+
+
+

+GET: /Clusters//ProteinMatrix +

+

Same as /Clusters/<cluster_variable>/SigProjMatrix/Normal, but for CITE proteins

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # proteins x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # proteins x cell group (+ 'Score') matrix of p-values
+    }
+
+
+

+GET: /Clusters/list

+

Not used anymore

+
+
+

+GET: /Clusters//Cells +

+

Not used anymore

+
+
+

+GET: /Expression/Genes/List

+

Retrieves a list of genes for which expression values can be plotted. Used to populate the dropdown in the ‘Genes’ tab.

+

Response structure:

+
[list of str - gene names]
+
+
+

+GET: /Expression/Gene/ +

+

Gets the per-cell expression of the gene specified by <gene_name>. Expression values returned are on a log2 scale.

+

Response structure: Items in ‘values’ correspond to the cells in ‘cells’ in order

+
    {
+        'cells': [list of str - cell identifiers],
+        'values': [list of number - gene expression values],
+    }
+
+
+

+GET: /Cell//Meta +

+

Retrieves meta-data information for an individual cell specified by <cell_id>

+

Response structure:

+
    {
+        'variable name': value (str or number),
+        'variable name': value (str or number),
+        'variable name': value (str or number),
+        ...
+    }
+
+
+

+POST: /Cells/Meta

+

Retrieves meta-data information for a group of cells

+

Posted data structure

+
[list of cell id]
+

Response structure:

+
    {
+        'numeric': {
+            '<variable name>': {
+                'Min': <min value>,
+                'Median': <median value>,
+                'Max': <max value>,
+            },
+            '<variable name>': {
+                'Min': <min value>,
+                'Median': <median value>,
+                'Max': <max value>,
+            },
+            # Repeat for additional numeric meta-data variables
+        },
+        'factor': {
+            '<variable name>': {
+                '<factor level 1>': number (proportion of cells assigned to this level,
+                '<factor level 2>': number (proportion of cells assigned to this level,
+                '<factor level 3>': number (proportion of cells assigned to this level,
+                ...
+            }
+            # Repeat for additional factor meta-data variables
+        }
+    }
+
+
+

+GET: /Cells/Selections

+

Used when loading a selection of cells.

+

Response structure:

+
[list of str - names of saved selections]
+
+
+

+GET: /Cells/Selections/ +

+

Retrieves the cells associated with the selection, <selection_id>

+

Response structure:

+
[list of str - cell ids in the indicated cell selection]
+
+
+

+POST: /Cells/Selections/ +

+

Saves a cell selection with name <selection_id>

+
[list of str - cell ids to be assigned to this cell selection]
+
+
+

+GET: /Tree/Projections/list

+

Get the list of different tree layouts that are available Used to populate the ‘Projection’ dropdown under the ‘Trajectories’ view

+

R version: returns the names of

+

Response structure:

+
[list of str - names of tree projections]
+
+
+

+GET: /Tree/Projections//coordinates +

+

Returns the coordinates for the tree layout <proj_name> in addition to the position of individual cells

+

Response structure:

+
    [
+        [
+            [<x val>, <y val>, <cell id>],  # coordinates for individual cells
+            [<x val>, <y val>, <cell id>],
+            [<x val>, <y val>, <cell id>],
+            ...
+        ],
+        [
+            [<x val>, <y val>],  # coordinates for internal tree nodes
+            [<x val>, <y val>], 
+            [<x val>, <y val>], 
+            ...
+        ],
+        [list of list of number]  # 0/1 adjacency matrix for internal tree nodes
+    ]
+
+
+

+GET: /Tree/SigProjMatrix/Normal

+

Returns matrices consisting of test statistic and p-value trajectory autocorrelation Format is similar to /Clusters/<cluster_variable>/SigProjMatrix/Normal, but without the 1 vs all test results.

+

‘zscores’ and ‘pvals’ matrices have just a single column

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # signatures x 1 matrix of test statistics
+        'pvals': [list of list of number] # signatures x 1 matrix of p-values
+    }
+
+
+

+GET: /Tree/SigProjMatrix/Meta

+

Same as /Tree/SigProjMatrix/Normal but for meta-data variables

+

‘zscores’ and ‘pvals’ matrices have just a single column

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # variables x 1 matrix of test statistics
+        'pvals': [list of list of number] # variables x 1 matrix of p-values
+    }
+
+
+

+GET: /Tree/ProteinMatrix

+

Same as /Tree/SigProjMatrix/Normal but for CITE protein expression values

+

‘zscores’ and ‘pvals’ matrices have just a single column

+

Response structure:

+
    {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # proteins x 1 matrix of test statistics
+        'pvals': [list of list of number] # proteins x 1 matrix of p-values
+    }
+
+ + +
+ + + +
+ + + +
+
+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 536364b6..6f105d34 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 @@ -89,7 +89,7 @@
  • - +
    • @@ -115,6 +115,12 @@
  • Incorporating a Trajectory Model
    • +
  • + PhyloVision and Hotspot +
    • +
  • + Spatial Data and Hotspot +
  • How To: Working with Seurat
    • @@ -133,7 +139,7 @@
    • - +
      • @@ -191,11 +197,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/articles/Signatures.html b/docs/articles/Signatures.html index acbc11e1..e3bc63d6 100644 --- a/docs/articles/Signatures.html +++ b/docs/articles/Signatures.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 @@ -47,7 +47,7 @@
      • - +
        • @@ -73,6 +73,12 @@
      • Incorporating a Trajectory Model
        • +
      • + PhyloVision and Hotspot +
        • +
      • + Spatial Data and Hotspot +
      • How To: Working with Seurat
        • @@ -91,7 +97,7 @@
        • - +
          • @@ -105,7 +111,7 @@ -
          +

          Gene Signatures

          @@ -145,27 +151,30 @@

          1. Creating a Signature object in R

          Once a set of genes that are up or down regulated in the process or cell type of interest are selected, creating a Signature object from them is relatively straightforward:

          -
          sigData <- c(
-    Gene.A = 1, Gene.B = 1, Gene.C = 1,
-    Gene.D = -1, Gene.B = -1, Gene.C = -1
-)
+
          +sigData <- c(
+    Gene.A = 1, Gene.B = 1, Gene.C = 1,
+    Gene.D = -1, Gene.B = -1, Gene.C = -1
+)
 
-sig <- createGeneSignature(name = "Interesting Process", sigData = sigData)
          
+sig <- createGeneSignature(name = "Interesting Process", sigData = sigData)

          For the sigData vector, the names represent gene names and the values (1 or -1) represent the ‘sign’ of the gene. For an unsigned signature, just use 1 for the value of every gene.

          A list of these sig objects can then be passed into the VISION object constructor instead of paths to .gmt files.

          -
          sig1 <- createGeneSignature(name = "Interesting Process", ... )
-sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
+
          +sig1 <- createGeneSignature(name = "Interesting Process", ... )
+sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
 
-mySignatures <- c(sig1, sig2)
+mySignatures <- c(sig1, sig2)
 
-vis <- Vision(data = expressionMat, signatures = mySignatures)
          
+vis <- Vision(data = expressionMat, signatures = mySignatures)

          Additionally, you can mix and match user-created signatures and paths to signature files in the signatures argument. When doing this, signatures in each library file are read and combined with the user-created signatures.

          -
          sig1 <- createGeneSignature(name = "Interesting Process", ... )
-sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
+
          +sig1 <- createGeneSignature(name = "Interesting Process", ... )
+sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
 
-mySignatures <- c(sig1, sig2, 'path/to/some/library.gmt')
+mySignatures <- c(sig1, sig2, 'path/to/some/library.gmt')
 
-vis <- Vision(data = expressionMat, signatures = mySignatures)
          
+vis <- Vision(data = expressionMat, signatures = mySignatures)

          @@ -218,11 +227,11 @@

          -

          Developed by Matt Jones, David Detomaso, Tal Ashuach.

          +

          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

          -

          Site built with pkgdown 1.5.1.

          +

          Site built with pkgdown 1.6.1.

          diff --git a/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js b/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html index 804a440a..5c18e746 100644 --- a/docs/articles/VISION-vignette.html +++ b/docs/articles/VISION-vignette.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0

          @@ -47,7 +47,7 @@
          @@ -47,7 +47,7 @@
          + + + + + + + + diff --git a/docs/reference/ServerExpression.html b/docs/reference/ServerExpression.html index 460e1209..2ab4ea66 100644 --- a/docs/reference/ServerExpression.html +++ b/docs/reference/ServerExpression.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0
          @@ -90,7 +90,7 @@
          • - +
            • @@ -116,6 +116,12 @@
          • Incorporating a Trajectory Model
            • +
          • + PhyloVision and Hotspot +
            • +
          • + Spatial Data and Hotspot +
          • How To: Working with Seurat
            • @@ -134,7 +140,7 @@
            • - +
              • @@ -160,7 +166,7 @@

              Wrapper class for gene expression object for JSON.

              Wrapper class for gene expression object for JSON.

              - 
              ServerExpression(data, sample_labels, gene_labels)
              + 
              ServerExpression(data, sample_labels, gene_labels)

              Arguments

              @@ -194,11 +200,11 @@

              Contents

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/ServerSigProjMatrix.html b/docs/reference/ServerSigProjMatrix.html index 4eb3a9ea..30333091 100644 --- a/docs/reference/ServerSigProjMatrix.html +++ b/docs/reference/ServerSigProjMatrix.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
              @@ -198,11 +204,11 @@

              Contents

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/Signature.html b/docs/reference/Signature.html index 3171cfd4..7d51ea83 100644 --- a/docs/reference/Signature.html +++ b/docs/reference/Signature.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
              @@ -198,11 +204,11 @@

              Contents

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/Trajectory.html b/docs/reference/Trajectory.html index 0cb0e53e..c197375b 100644 --- a/docs/reference/Trajectory.html +++ b/docs/reference/Trajectory.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
              @@ -187,11 +193,11 @@

              Contents

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/TrajectoryProjection.html b/docs/reference/TrajectoryProjection.html index 5c7915af..09bc6e27 100644 --- a/docs/reference/TrajectoryProjection.html +++ b/docs/reference/TrajectoryProjection.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
              @@ -198,11 +204,11 @@

              Contents

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/VISION-class.html b/docs/reference/VISION-class.html index f4b26d0d..1a8369e6 100644 --- a/docs/reference/VISION-class.html +++ b/docs/reference/VISION-class.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
              • - +
                • @@ -119,6 +119,12 @@
              • Incorporating a Trajectory Model
                • +
              • + PhyloVision and Hotspot +
                • +
              • + Spatial Data and Hotspot +
              • How To: Working with Seurat
                • @@ -137,7 +143,7 @@
                • - +
                  • @@ -166,55 +172,56 @@

                  Initializes a new VISION object.

                  expression data, meta-data, and dimensionality reductions if they exist already

                  - 
                  Vision(data, ...)
+    
                  Vision(data, ...)
 
 # S4 method for matrixORSparse
-Vision(
-  data,
-  signatures = list(),
-  proteinData = NULL,
-  unnormalizedData = NULL,
-  meta = NULL,
-  projection_genes = c("fano"),
-  min_signature_genes = 5,
-  sig_gene_threshold = 0.001,
-  threshold = 0.05,
-  perm_wPCA = FALSE,
-  projection_methods = c("tSNE30"),
-  sig_norm_method = c("znorm_columns", "none", "znorm_rows", "znorm_rows_then_columns",
-    "rank_norm_columns"),
-  pool = "auto",
-  cellsPerPartition = 10,
-  name = NULL,
-  num_neighbors = NULL,
-  latentSpace = NULL,
-  latentSpaceName = NULL,
-  latentTrajectory = NULL,
-  tree = NULL,
-  modData = list(),
-  pools = list()
-)
+Vision(
+  data,
+  signatures = list(),
+  proteinData = NULL,
+  unnormalizedData = NULL,
+  meta = NULL,
+  projection_genes = c("fano"),
+  min_signature_genes = 5,
+  sig_gene_threshold = 0.001,
+  threshold = 0.05,
+  perm_wPCA = FALSE,
+  projection_methods = c("tSNE30"),
+  sig_norm_method = c("znorm_columns", "none", "znorm_rows", "znorm_rows_then_columns",
+    "rank_norm_columns"),
+  pool = "auto",
+  cellsPerPartition = 10,
+  name = NULL,
+  num_neighbors = NULL,
+  latentSpace = NULL,
+  latentSpaceName = NULL,
+  latentTrajectory = NULL,
+  tree = NULL,
+  modData = list(),
+  hotspot = NULL,
+  pools = list()
+)
 
 # S4 method for data.frame
-Vision(data, ...)
+Vision(data, ...)
 
 # S4 method for sparseMatrix
-Vision(data, ...)
+Vision(data, ...)
 
 # S4 method for dgeMatrix
-Vision(data, ...)
+Vision(data, ...)
 
 # S4 method for ExpressionSet
-Vision(data, ...)
+Vision(data, ...)
 
 # S4 method for SummarizedExperiment
-Vision(data, ...)
+Vision(data, ...)
 
 # S4 method for seurat
-Vision(data, dimRed = NULL, dimRedComponents = NULL, ...)
+Vision(data, dimRed = NULL, dimRedComponents = NULL, ...)
 
 # S4 method for Seurat
-Vision(data, assay = "RNA", dimRed = NULL, dimRedComponents = NULL, ...)
                  
+Vision(data, assay = "RNA", dimRed = NULL, dimRedComponents = NULL, ...)

                  Arguments

              @@ -338,6 +345,10 @@

              Arg

              + + + +
              modData

              a list of signature objects for user defined modules
              hotspot

              a list containing one hotspot object precomputed in python and loaded in via reticulate

              pools

              assignments of cell to micropool. Used when microclustering batches @@ -364,19 +375,20 @@

              Value

              A VISION object

              Examples

              - 
              if (FALSE) {
-expMat <- read.csv("expressionMatrix.csv", row.names=1)
-meta <- read.csv("metaData.csv", row.names=1)
+    
              if (FALSE) {
+expMat <- read.csv("expressionMatrix.csv", row.names=1)
+meta <- read.csv("metaData.csv", row.names=1)
 
-sigs <- c("/path/to/signatures/msigdb_Hallmark.gmt",
+sigs <- c("/path/to/signatures/msigdb_Hallmark.gmt",
           "/path/to/signatures/Enrichr/ChEA_2015.txt"
-         )
+         )
 
 
-vis <- Vision(data = expMat,
-              signatures = sigs,
-              meta = meta)
-}
              
+vis <- Vision(data = expMat,
+              signatures = sigs,
+              meta = meta)
+}
+
              @@ -96,7 +96,7 @@
              • - +
                • @@ -122,6 +122,12 @@
              • Incorporating a Trajectory Model
                • +
              • + PhyloVision and Hotspot +
                • +
              • + Spatial Data and Hotspot +
              • How To: Working with Seurat
                • @@ -140,7 +146,7 @@
                • - +
                  • @@ -186,11 +192,11 @@

                  Contents

                  -

                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                  +

                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                  -

                  Site built with pkgdown 1.5.1.

                  +

                  Site built with pkgdown 1.6.1.

                  diff --git a/docs/reference/addHotspotToVision.html b/docs/reference/addHotspotToVision.html new file mode 100644 index 00000000..30873b22 --- /dev/null +++ b/docs/reference/addHotspotToVision.html @@ -0,0 +1,215 @@ + + + + + + + + +Add HS python obj to vision OBJECT — addHotspotToVision • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                  +
                  + + + + +
                  + +
                  +
                  +
                  +

                  Add HS python obj to vision OBJECT

                  + Source: R/methods-Module.R + +
                  + +
                  +

                  Add HS python obj to vision OBJECT

                  +
                  + + 
                  addHotspotToVision(object, hs)
                  + +

                  Arguments

                  + + + + + + + + + + +
                  object

                  Vision object

                  hs

                  python hs object

                  + +

                  Value

                  + +

                  Vision object with hs populated

                  + +
                  + +
                  + + +
                  +
                  +

                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                  +
                  + +
                  +

                  Site built with pkgdown 1.6.1.

                  +
                  + +
                  +
                  + + + + + + + + diff --git a/docs/reference/addLatentSpace.html b/docs/reference/addLatentSpace.html index a5060199..0d07ee4e 100644 --- a/docs/reference/addLatentSpace.html +++ b/docs/reference/addLatentSpace.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                  • - +
                    • @@ -116,6 +116,12 @@
                  • Incorporating a Trajectory Model
                    • +
                  • + PhyloVision and Hotspot +
                    • +
                  • + Spatial Data and Hotspot +
                  • How To: Working with Seurat
                    • @@ -134,7 +140,7 @@
                    • - +
                      • @@ -160,7 +166,7 @@

                      Add a latent space computed using an external method

                      Add a latent space computed using an external method

                      - 
                      addLatentSpace(object, coordinates, name)
                      + 
                      addLatentSpace(object, coordinates, name)

                      Arguments

                      @@ -194,11 +200,11 @@

                      Contents

                      -

                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                      +

                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                      -

                      Site built with pkgdown 1.5.1.

                      +

                      Site built with pkgdown 1.6.1.

                      diff --git a/docs/reference/addProjection-Vision-method.html b/docs/reference/addProjection-Vision-method.html index d4ae7500..c68048b0 100644 --- a/docs/reference/addProjection-Vision-method.html +++ b/docs/reference/addProjection-Vision-method.html @@ -87,7 +87,7 @@ VISION - 2.1.0 + 3.0.0 @@ -95,7 +95,7 @@
                      @@ -196,22 +202,23 @@

                      Value

                      VISION object

                      Examples

                      - 
                      if (FALSE) {
+    
                      if (FALSE) {
 
 # First create the VISION object
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
 # Load and add an additional visualization
-my_umap <- read.csv("umap_results.csv")
-vis <- addProjection(vis, "UMAP", my_umap)
+my_umap <- read.csv("umap_results.csv")
+vis <- addProjection(vis, "UMAP", my_umap)
 
 # Run analysis
-vis <- analyze(vis)
+vis <- analyze(vis)
 
 # View results
-viewResults(vis)
+viewResults(vis)
 
-}
                      
+}
+
                      @@ -90,7 +90,7 @@
                      @@ -207,11 +213,11 @@

                      Contents

                      -

                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                      +

                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                      -

                      Site built with pkgdown 1.5.1.

                      +

                      Site built with pkgdown 1.6.1.

                      diff --git a/docs/reference/addTSNE.html b/docs/reference/addTSNE.html index c37a37c0..57e89357 100644 --- a/docs/reference/addTSNE.html +++ b/docs/reference/addTSNE.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                      @@ -199,11 +205,11 @@

                      Contents

                      -

                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                      +

                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                      -

                      Site built with pkgdown 1.5.1.

                      +

                      Site built with pkgdown 1.6.1.

                      diff --git a/docs/reference/addUMAP.html b/docs/reference/addUMAP.html index e9ed30e8..5c852d96 100644 --- a/docs/reference/addUMAP.html +++ b/docs/reference/addUMAP.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                      @@ -204,11 +210,11 @@

                      Contents

                      -

                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                      +

                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                      -

                      Site built with pkgdown 1.5.1.

                      +

                      Site built with pkgdown 1.6.1.

                      diff --git a/docs/reference/analyze-Vision-method.html b/docs/reference/analyze-Vision-method.html index e5f59727..f9bff987 100644 --- a/docs/reference/analyze-Vision-method.html +++ b/docs/reference/analyze-Vision-method.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                      @@ -174,7 +180,7 @@

                      Arg

                      - +
                      tree

                      wether to use the TREE slot of the object to calculate values

                      whether to use the TREE slot of the object to calculate values
                      @@ -183,14 +189,15 @@

                      Value

                      VISION object

                      Examples

                      - 
                      if (FALSE) {
+    
                      if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-}
                      
+}
+
                      @@ -93,7 +93,7 @@
                      • - +
                        • @@ -119,6 +119,12 @@
                      • Incorporating a Trajectory Model
                        • +
                      • + PhyloVision and Hotspot +
                        • +
                      • + Spatial Data and Hotspot +
                      • How To: Working with Seurat
                        • @@ -137,7 +143,7 @@
                        • - +
                          • @@ -166,7 +172,7 @@

                          Compute local correlations for all signatures

                          to find signals that are captured succesfully by the projections.

                          - 
                          analyzeLocalCorrelations(object, tree = FALSE)
                          + 
                          analyzeLocalCorrelations(object, tree = FALSE)

                          Arguments

                          @@ -192,11 +198,11 @@

                          Contents

                          -

                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                          +

                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                          -

                          Site built with pkgdown 1.5.1.

                          +

                          Site built with pkgdown 1.6.1.

                          diff --git a/docs/reference/analyzeLocalCorrelationsModules.html b/docs/reference/analyzeLocalCorrelationsModules.html new file mode 100644 index 00000000..c294bb50 --- /dev/null +++ b/docs/reference/analyzeLocalCorrelationsModules.html @@ -0,0 +1,221 @@ + + + + + + + + +Compute local correlations for all modules — analyzeLocalCorrelationsModules • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                          +
                          + + + + +
                          + +
                          +
                          +
                          +

                          Compute local correlations for all modules

                          + Source: R/methods-Module.R + +
                          + +
                          +

                          This is the main analysis function. For each filtered dataset, a set of +different projection onto low-dimensional space are computed, and the +consistency of the resulting space with the signature scores is computed +to find signals that are captured successfully by the projections.

                          +
                          + + 
                          analyzeLocalCorrelationsModules(object, tree = FALSE)
                          + +

                          Arguments

                          +
                          + + + + + + + + + +
                          object

                          the VISION object

                          tree

                          whether to use the tree object as latent space for neighbors

                          + +

                          Value

                          + +

                          the VISION object with values set for the analysis results

                          + + + + + + +
                          +
                          +

                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                          +
                          + +
                          +

                          Site built with pkgdown 1.6.1.

                          +
                          + +
                          + + + + + + + + + diff --git a/docs/reference/analyzeTrajectoryCorrelations.html b/docs/reference/analyzeTrajectoryCorrelations.html index 32facc07..01750d27 100644 --- a/docs/reference/analyzeTrajectoryCorrelations.html +++ b/docs/reference/analyzeTrajectoryCorrelations.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                          • - +
                            • @@ -119,6 +119,12 @@
                          • Incorporating a Trajectory Model
                            • +
                          • + PhyloVision and Hotspot +
                            • +
                          • + Spatial Data and Hotspot +
                          • How To: Working with Seurat
                            • @@ -137,7 +143,7 @@
                            • - +
                              • @@ -166,7 +172,7 @@

                              Compute trajectory correlations for all signatures

                              to find signals that are captured succesfully by the projections.

                              - 
                              analyzeTrajectoryCorrelations(object)
                              + 
                              analyzeTrajectoryCorrelations(object)

                              Arguments

                              @@ -192,11 +198,11 @@

                              Contents

                              -

                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                              +

                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                              -

                              Site built with pkgdown 1.5.1.

                              +

                              Site built with pkgdown 1.6.1.

                              diff --git a/docs/reference/ancestor_at_depth.html b/docs/reference/ancestor_at_depth.html new file mode 100644 index 00000000..6a85ddbb --- /dev/null +++ b/docs/reference/ancestor_at_depth.html @@ -0,0 +1,219 @@ + + + + + + + + +Find the ancestor of a node above a specific depth — ancestor_at_depth • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                              +
                              + + + + +
                              + +
                              +
                              +
                              +

                              Find the ancestor of a node above a specific depth

                              + Source: R/Utilities.R + +
                              + +
                              +

                              Find the ancestor of a node above a specific depth

                              +
                              + + 
                              ancestor_at_depth(tree, node, depth)
                              + +

                              Arguments

                              +
                              + + + + + + + + + + + + + +
                              tree

                              an object of class phylo

                              node

                              the index of the node

                              depth

                              the depth to search to

                              + +

                              Value

                              + +

                              the index of the ancestor node

                              + + + + + + +
                              +
                              +

                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                              +
                              + +
                              +

                              Site built with pkgdown 1.6.1.

                              +
                              + +
                              + + + + + + + + + diff --git a/docs/reference/annotateLatentComponents.html b/docs/reference/annotateLatentComponents.html index db0abab0..a85740a5 100644 --- a/docs/reference/annotateLatentComponents.html +++ b/docs/reference/annotateLatentComponents.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                              • - +
                                • @@ -116,6 +116,12 @@
                              • Incorporating a Trajectory Model
                                • +
                              • + PhyloVision and Hotspot +
                                • +
                              • + Spatial Data and Hotspot +
                              • How To: Working with Seurat
                                • @@ -134,7 +140,7 @@
                                • - +
                                  • @@ -160,7 +166,7 @@

                                  Compute pearson correlation between signature scores and components of the L

                                  Enables the LCAnnotator portion of the output report

                                  - 
                                  annotateLatentComponents(object)
                                  + 
                                  annotateLatentComponents(object)

                                  Arguments

                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyFilters.html b/docs/reference/applyFilters.html index f442cc3c..bdc8c392 100644 --- a/docs/reference/applyFilters.html +++ b/docs/reference/applyFilters.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -198,11 +204,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyICA.html b/docs/reference/applyICA.html index 61ac55e9..caeceb23 100644 --- a/docs/reference/applyICA.html +++ b/docs/reference/applyICA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyISOMap.html b/docs/reference/applyISOMap.html index b013cb73..23853220 100644 --- a/docs/reference/applyISOMap.html +++ b/docs/reference/applyISOMap.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyMicroClustering.html b/docs/reference/applyMicroClustering.html index e88f30d7..f3ec3806 100644 --- a/docs/reference/applyMicroClustering.html +++ b/docs/reference/applyMicroClustering.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -228,11 +234,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyPCA.html b/docs/reference/applyPCA.html index 4fa2f876..2d342ad8 100644 --- a/docs/reference/applyPCA.html +++ b/docs/reference/applyPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -192,11 +198,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyPermutationWPCA.html b/docs/reference/applyPermutationWPCA.html index 0e5e5d91..091a97a9 100644 --- a/docs/reference/applyPermutationWPCA.html +++ b/docs/reference/applyPermutationWPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -204,11 +210,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyRBFPCA.html b/docs/reference/applyRBFPCA.html index c0edab8f..16fd9ae5 100644 --- a/docs/reference/applyRBFPCA.html +++ b/docs/reference/applyRBFPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applySimplePPT.html b/docs/reference/applySimplePPT.html index 239ee442..9149ede4 100644 --- a/docs/reference/applySimplePPT.html +++ b/docs/reference/applySimplePPT.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -227,11 +233,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applySpectralEmbedding.html b/docs/reference/applySpectralEmbedding.html index 169fb92e..b3896820 100644 --- a/docs/reference/applySpectralEmbedding.html +++ b/docs/reference/applySpectralEmbedding.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applyUMAP.html b/docs/reference/applyUMAP.html index ca47e3e3..121d6f00 100644 --- a/docs/reference/applyUMAP.html +++ b/docs/reference/applyUMAP.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -190,11 +196,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applytSNE10.html b/docs/reference/applytSNE10.html index c26dfe74..d0ae0f8a 100644 --- a/docs/reference/applytSNE10.html +++ b/docs/reference/applytSNE10.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/applytSNE30.html b/docs/reference/applytSNE30.html index b1e45351..aa14d7f8 100644 --- a/docs/reference/applytSNE30.html +++ b/docs/reference/applytSNE30.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -186,11 +192,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/batchSigEvalNorm.html b/docs/reference/batchSigEvalNorm.html index b36fc1c9..773a37fd 100644 --- a/docs/reference/batchSigEvalNorm.html +++ b/docs/reference/batchSigEvalNorm.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                  @@ -192,11 +198,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/batchify.html b/docs/reference/batchify.html index d332f181..56fe6136 100644 --- a/docs/reference/batchify.html +++ b/docs/reference/batchify.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 @@ -92,7 +92,7 @@
                                  @@ -197,11 +203,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/calcInterEdgeDistMat.html b/docs/reference/calcInterEdgeDistMat.html index 169b4d9d..c511c4b8 100644 --- a/docs/reference/calcInterEdgeDistMat.html +++ b/docs/reference/calcInterEdgeDistMat.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -196,11 +202,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/calcIntraEdgeDistMat.html b/docs/reference/calcIntraEdgeDistMat.html index abacc5c8..43f52d49 100644 --- a/docs/reference/calcIntraEdgeDistMat.html +++ b/docs/reference/calcIntraEdgeDistMat.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                  @@ -190,11 +196,11 @@

                                  Contents

                                  -

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  -

                                  Site built with pkgdown 1.5.1.

                                  +

                                  Site built with pkgdown 1.6.1.

                                  diff --git a/docs/reference/calcModuleScores.html b/docs/reference/calcModuleScores.html new file mode 100644 index 00000000..c463159f --- /dev/null +++ b/docs/reference/calcModuleScores.html @@ -0,0 +1,226 @@ + + + + + + + + +Calculate module scores (signature scores but on the modules) — calcModuleScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                  +
                                  + + + + +
                                  + +
                                  +
                                  +
                                  +

                                  Calculate module scores (signature scores but on the modules)

                                  + Source: R/methods-Module.R + +
                                  + +
                                  +

                                  For each module-cell pair, compute a score that captures the level of +correspondence between the cell and the module.

                                  +
                                  + + 
                                  calcModuleScores(object, mod_norm_method = NULL, mod_gene_importance = TRUE)
                                  + +

                                  Arguments

                                  +
                                  + + + + + + + + + + + + + +
                                  object

                                  the VISION object

                                  mod_norm_method

                                  Method to apply to normalize the expression matrix +before calculating signature scores. Valid options are: +"znorm_columns" (default), "none", "znorm_rows", "znorm_rows_then_columns", +or "rank_norm_columns"

                                  mod_gene_importance

                                  whether or not to rank each gene's contribution to +the overall signature score. Default = TRUE. This is used for inspecting +genes in a signature in the output report

                                  + +

                                  Value

                                  + +

                                  the VISION object, with the @ModScores and @ModGeneImportance slots populated

                                  + + + + + + +
                                  +
                                  +

                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                  +
                                  + +
                                  +

                                  Site built with pkgdown 1.6.1.

                                  +
                                  + +
                                  + + + + + + + + + diff --git a/docs/reference/calcSignatureScores.html b/docs/reference/calcSignatureScores.html index f3a4ba8c..803c779c 100644 --- a/docs/reference/calcSignatureScores.html +++ b/docs/reference/calcSignatureScores.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                  • - +
                                    • @@ -117,6 +117,12 @@
                                  • Incorporating a Trajectory Model
                                    • +
                                  • + PhyloVision and Hotspot +
                                    • +
                                  • + Spatial Data and Hotspot +
                                  • How To: Working with Seurat
                                    • @@ -135,7 +141,7 @@
                                    • - +
                                      • @@ -162,7 +168,7 @@

                                      calculate signature scores

                                      correspondence between the cell and the signature.

                                      - 
                                      calcSignatureScores(object, sig_norm_method = NULL, sig_gene_importance = TRUE)
                                      + 
                                      calcSignatureScores(object, sig_norm_method = NULL, sig_gene_importance = TRUE)

                                      Arguments

                                      @@ -201,11 +207,11 @@

                                      Contents

                                      -

                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                      +

                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                      -

                                      Site built with pkgdown 1.5.1.

                                      +

                                      Site built with pkgdown 1.6.1.

                                      diff --git a/docs/reference/calc_mod_sig_enrichment.html b/docs/reference/calc_mod_sig_enrichment.html new file mode 100644 index 00000000..eed30fac --- /dev/null +++ b/docs/reference/calc_mod_sig_enrichment.html @@ -0,0 +1,215 @@ + + + + + + + + +Computes the hypergeometric overlap test for modules and signatures — calc_mod_sig_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                      +
                                      + + + + +
                                      + +
                                      +
                                      +
                                      +

                                      Computes the hypergeometric overlap test for modules and signatures

                                      + Source: R/methods-Module.R + +
                                      + +
                                      +

                                      Computes the hypergeometric overlap test for modules and signatures

                                      +
                                      + + 
                                      calc_mod_sig_enrichment(object, skip_down = TRUE)
                                      + +

                                      Arguments

                                      +
                                      + + + + + + + + + +
                                      object

                                      the Vision object.

                                      skip_down

                                      whether to ignore down signatures in overlap

                                      + +

                                      Value

                                      + +

                                      list(statistic values, p values, clusters of signatures)

                                      + + + + + + +
                                      +
                                      +

                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                      +
                                      + +
                                      +

                                      Site built with pkgdown 1.6.1.

                                      +
                                      + +
                                      + + + + + + + + + diff --git a/docs/reference/calc_set_enrichment.html b/docs/reference/calc_set_enrichment.html new file mode 100644 index 00000000..cbf8978f --- /dev/null +++ b/docs/reference/calc_set_enrichment.html @@ -0,0 +1,229 @@ + + + + + + + + +Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) — calc_set_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                      +
                                      + + + + +
                                      + +
                                      +
                                      +
                                      +

                                      Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|))

                                      + Source: R/methods-Module.R + +
                                      + +
                                      +

                                      Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|))

                                      +
                                      + + 
                                      calc_set_enrichment(set1, set2, genes)
                                      + +

                                      Arguments

                                      + + + + + + + + + + + + + + +
                                      set1

                                      the first gene set

                                      set2

                                      the second gene set

                                      genes

                                      the population

                                      + +

                                      Value

                                      + +

                                      c(statistic, p value)

                                      + +
                                      + +
                                      + + +
                                      +
                                      +

                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                      +
                                      + +
                                      +

                                      Site built with pkgdown 1.6.1.

                                      +
                                      + +
                                      +
                                      + + + + + + + + diff --git a/docs/reference/calculateTrajectoryDistances.html b/docs/reference/calculateTrajectoryDistances.html index 305662a8..f62f7bfe 100644 --- a/docs/reference/calculateTrajectoryDistances.html +++ b/docs/reference/calculateTrajectoryDistances.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                      • - +
                                        • @@ -116,6 +116,12 @@
                                      • Incorporating a Trajectory Model
                                        • +
                                      • + PhyloVision and Hotspot +
                                        • +
                                      • + Spatial Data and Hotspot +
                                      • How To: Working with Seurat
                                        • @@ -134,7 +140,7 @@
                                        • - +
                                          • @@ -160,7 +166,7 @@

                                          Calculate distance matrix between all pairs of ponts based on their projecti

                                          Calculate distance matrix between all pairs of ponts based on their projection onto the tree

                                          - 
                                          calculateTrajectoryDistances(adjMat, edgeAssoc, edgePos, latentPnts = NULL)
                                          + 
                                          calculateTrajectoryDistances(adjMat, edgeAssoc, edgePos, latentPnts = NULL)

                                          Arguments

                                          @@ -198,11 +204,11 @@

                                          Contents

                                          -

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                          +

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                          -

                                          Site built with pkgdown 1.5.1.

                                          +

                                          Site built with pkgdown 1.6.1.

                                          diff --git a/docs/reference/clipBottom.html b/docs/reference/clipBottom.html index b4f09253..c311c23e 100644 --- a/docs/reference/clipBottom.html +++ b/docs/reference/clipBottom.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                          @@ -190,11 +196,11 @@

                                          Contents

                                          -

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                          +

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                          -

                                          Site built with pkgdown 1.5.1.

                                          +

                                          Site built with pkgdown 1.6.1.

                                          diff --git a/docs/reference/clusterCells.html b/docs/reference/clusterCells.html index c8e61a43..0961837f 100644 --- a/docs/reference/clusterCells.html +++ b/docs/reference/clusterCells.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                          @@ -186,11 +192,11 @@

                                          Contents

                                          -

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                          +

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                          -

                                          Site built with pkgdown 1.5.1.

                                          +

                                          Site built with pkgdown 1.6.1.

                                          diff --git a/docs/reference/clusterModScores.html b/docs/reference/clusterModScores.html new file mode 100644 index 00000000..b5b26422 --- /dev/null +++ b/docs/reference/clusterModScores.html @@ -0,0 +1,215 @@ + + + + + + + + +Compute Ranksums Test, for all factor meta data. One level vs all others — clusterModScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                          +
                                          + + + + +
                                          + +
                                          +
                                          +
                                          +

                                          Compute Ranksums Test, for all factor meta data. One level vs all others

                                          + Source: R/methods-Module.R + +
                                          + +
                                          +

                                          Compute Ranksums Test, for all factor meta data. One level vs all others

                                          +
                                          + + 
                                          clusterModScores(object, variables = "All")
                                          + +

                                          Arguments

                                          +
                                          + + + + + + + + + +
                                          object

                                          the VISION object

                                          variables

                                          which columns of the meta-data to use for comparisons

                                          + +

                                          Value

                                          + +

                                          the VISION object with the @ClusterComparisons modules slot populated

                                          + + + + + + +
                                          +
                                          +

                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                          +
                                          + +
                                          +

                                          Site built with pkgdown 1.6.1.

                                          +
                                          + +
                                          + + + + + + + + + diff --git a/docs/reference/clusterSigScores.html b/docs/reference/clusterSigScores.html index 25ca1429..fb852aaa 100644 --- a/docs/reference/clusterSigScores.html +++ b/docs/reference/clusterSigScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                          • - +
                                            • @@ -116,6 +116,12 @@
                                          • Incorporating a Trajectory Model
                                            • +
                                          • + PhyloVision and Hotspot +
                                            • +
                                          • + Spatial Data and Hotspot +
                                          • How To: Working with Seurat
                                            • @@ -134,7 +140,7 @@
                                            • - +
                                              • @@ -160,7 +166,7 @@

                                              Compute Ranksums Test, for all factor meta data. One level vs all othersCompute Ranksums Test, for all factor meta data. One level vs all others

                                              - 
                                              clusterSigScores(object, variables = "All")
                                              + 
                                              clusterSigScores(object, variables = "All")

                                              Arguments

                                              @@ -190,11 +196,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/clusterSignatures.html b/docs/reference/clusterSignatures.html index 4ea14ea0..45983b91 100644 --- a/docs/reference/clusterSignatures.html +++ b/docs/reference/clusterSignatures.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -202,11 +208,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/colNormalization.html b/docs/reference/colNormalization.html index 19427e26..ad23cdf3 100644 --- a/docs/reference/colNormalization.html +++ b/docs/reference/colNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -186,11 +192,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/colRankNormalization.html b/docs/reference/colRankNormalization.html index ff2b0ee7..4d2004f5 100644 --- a/docs/reference/colRankNormalization.html +++ b/docs/reference/colRankNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -186,11 +192,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/colVarsSp.html b/docs/reference/colVarsSp.html index 8a81d72d..872f73e2 100644 --- a/docs/reference/colVarsSp.html +++ b/docs/reference/colVarsSp.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -186,11 +192,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/computeKNNWeights-Trajectory-method.html b/docs/reference/computeKNNWeights-Trajectory-method.html index 35d61adb..3076c98c 100644 --- a/docs/reference/computeKNNWeights-Trajectory-method.html +++ b/docs/reference/computeKNNWeights-Trajectory-method.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -195,11 +201,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/computeKNNWeights-matrix-method.html b/docs/reference/computeKNNWeights-matrix-method.html index fa4d215f..f846e62f 100644 --- a/docs/reference/computeKNNWeights-matrix-method.html +++ b/docs/reference/computeKNNWeights-matrix-method.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              @@ -195,11 +201,11 @@

                                              Contents

                                              -

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              -

                                              Site built with pkgdown 1.5.1.

                                              +

                                              Site built with pkgdown 1.6.1.

                                              diff --git a/docs/reference/computeKNNWeights-phylo-method.html b/docs/reference/computeKNNWeights-phylo-method.html new file mode 100644 index 00000000..4861a703 --- /dev/null +++ b/docs/reference/computeKNNWeights-phylo-method.html @@ -0,0 +1,230 @@ + + + + + + + + +Compute for each vector the weights to apply to it's K nearest neighbors — computeKNNWeights,phylo-method • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                              +
                                              + + + + +
                                              + +
                                              +
                                              +
                                              +

                                              Compute for each vector the weights to apply to it's K nearest neighbors

                                              + Source: R/Projections.R + +
                                              + +
                                              +

                                              Compute for each vector the weights to apply to it's K nearest neighbors

                                              +
                                              + + 
                                              # S4 method for phylo
+computeKNNWeights(
+  object,
+  K = round(sqrt(length(object$tip.label))),
+  lcaKNN = FALSE,
+  minSize = 20
+)
                                              + +

                                              Arguments

                                              +
                                              + + + + + + + + + + + + + +
                                              object

                                              tree to use for KNN

                                              K

                                              Number of neighbors to consider.

                                              lcaKNN

                                              whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). +WARNING: lcaKNN doesn't perform well with broad multifurcations

                                              + +

                                              Value

                                              + +

                                              a list of two items: + indices: matrix, cells X neighbors + Each row specifies indices of nearest neighbors + weights: matrix, cells X neighbors + Corresponding weights to nearest neighbors

                                              + + + + + + +
                                              +
                                              +

                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                              +
                                              + +
                                              +

                                              Site built with pkgdown 1.6.1.

                                              +
                                              + +
                                              + + + + + + + + + diff --git a/docs/reference/computeLatentSpace.html b/docs/reference/computeLatentSpace.html index 1a38c56e..6cc19eda 100644 --- a/docs/reference/computeLatentSpace.html +++ b/docs/reference/computeLatentSpace.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                              • - +
                                                • @@ -116,6 +116,12 @@
                                              • Incorporating a Trajectory Model
                                                • +
                                              • + PhyloVision and Hotspot +
                                                • +
                                              • + Spatial Data and Hotspot +
                                              • How To: Working with Seurat
                                                • @@ -134,7 +140,7 @@
                                                • - +
                                                  • @@ -160,15 +166,15 @@

                                                  Computes the latent space of the expression matrix using PCA

                                                  Computes the latent space of the expression matrix using PCA

                                                  - 
                                                  computeLatentSpace(
-  object,
-  projection_genes = NULL,
-  filterThreshold = 0.05,
-  filterNumMad = 2,
-  projection_genes_method = NULL,
-  num_PCs = 30,
-  perm_wPCA = NULL
-)
                                                  + 
                                                  computeLatentSpace(
+  object,
+  projection_genes = NULL,
+  filterThreshold = 0.05,
+  filterNumMad = 2,
+  projection_genes_method = NULL,
+  num_PCs = 30,
+  perm_wPCA = NULL
+)

                                                  Arguments

                                                  @@ -222,11 +228,11 @@

                                                  Contents

                                                  -

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  -

                                                  Site built with pkgdown 1.5.1.

                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  diff --git a/docs/reference/computeProjectionGenes.html b/docs/reference/computeProjectionGenes.html index 0a76e9cd..78f3e751 100644 --- a/docs/reference/computeProjectionGenes.html +++ b/docs/reference/computeProjectionGenes.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                  @@ -212,11 +218,11 @@

                                                  Contents

                                                  -

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  -

                                                  Site built with pkgdown 1.5.1.

                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  diff --git a/docs/reference/convertGeneIds.html b/docs/reference/convertGeneIds.html index e599c5d1..25b8e60c 100644 --- a/docs/reference/convertGeneIds.html +++ b/docs/reference/convertGeneIds.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                  @@ -189,14 +195,16 @@

                                                  Details

                                                  Examples

                                                  -exp <- matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3), nrow=3)
-colnames(exp) <- c("Cell1", "Cell2", "Cell3")
-print(exp)
+exp <- matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3), nrow=3)
+colnames(exp) <- c("Cell1", "Cell2", "Cell3")
+print(exp)
+
+newIds <- c("GeneA", "GeneA", "GeneB")
 
-newIds <- c("GeneA", "GeneA", "GeneB")
+result <- convertGeneIds(exp, newIds)
+print(result)
 
-result <- convertGeneIds(exp, newIds)
-print(result)
                                                  + @@ -90,7 +90,7 @@
                                                  @@ -186,11 +192,11 @@

                                                  Contents

                                                  -

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  -

                                                  Site built with pkgdown 1.5.1.

                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  diff --git a/docs/reference/createGeneSignature.html b/docs/reference/createGeneSignature.html index 925221c6..d2df6692 100644 --- a/docs/reference/createGeneSignature.html +++ b/docs/reference/createGeneSignature.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                                                  @@ -193,21 +199,22 @@

                                                  Value

                                                  a Signature object

                                                  Examples

                                                  - 
                                                  if (FALSE) {
-sig1 <- createGeneSignature(
-           name = "CD8 Markers",
-           sigData = c(CD8A=1, CD8B=1, GZMK=1, GZMB=1,
-                       GZMH=1, GZMA=1, GNLY=1, DUSP2=1,
-                       EOMES=1, TBX21=1, PRMD1=1, PRF1=1,
-                       IFNG=1)
-       )
-
-cc_sigs <- "path/to/cell_cycle.gmt"
-
-sigs <- c(sig1, cc_sigs)
-
-vis <- Vision(data = expMat, signatures = sigs)
-}
                                                  + 
                                                  if (FALSE) {
+sig1 <- createGeneSignature(
+           name = "CD8 Markers",
+           sigData = c(CD8A=1, CD8B=1, GZMK=1, GZMB=1,
+                       GZMH=1, GZMA=1, GNLY=1, DUSP2=1,
+                       EOMES=1, TBX21=1, PRMD1=1, PRF1=1,
+                       IFNG=1)
+       )
+
+cc_sigs <- "path/to/cell_cycle.gmt"
+
+sigs <- c(sig1, cc_sigs)
+
+vis <- Vision(data = expMat, signatures = sigs)
+}
+
                                                  @@ -91,7 +91,7 @@
                                                  @@ -188,11 +194,11 @@

                                                  Contents

                                                  -

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  -

                                                  Site built with pkgdown 1.5.1.

                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  diff --git a/docs/reference/depthBasedCladewiseTreeCluster.html b/docs/reference/depthBasedCladewiseTreeCluster.html new file mode 100644 index 00000000..7aee7cee --- /dev/null +++ b/docs/reference/depthBasedCladewiseTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth. — depthBasedCladewiseTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                  +
                                                  + + + + +
                                                  + +
                                                  +
                                                  +
                                                  +

                                                  Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth.

                                                  + Source: R/Microclusters.R + +
                                                  + +
                                                  +

                                                  Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth.

                                                  +
                                                  + + 
                                                  depthBasedCladewiseTreeCluster(tree, target = 10)
                                                  + +

                                                  Arguments

                                                  +
                                                  + + + + + + + + + +
                                                  tree

                                                  object of class phylo

                                                  target

                                                  number of clusters to attempt to generate

                                                  + +

                                                  Value

                                                  + +

                                                  List of clusters, each entry being a vector of indices representing +samples in the cluster.

                                                  + + + + + + +
                                                  +
                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  +
                                                  + +
                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  +
                                                  + +
                                                  + + + + + + + + + diff --git a/docs/reference/depthBasedTreeCluster.html b/docs/reference/depthBasedTreeCluster.html new file mode 100644 index 00000000..9134f6d3 --- /dev/null +++ b/docs/reference/depthBasedTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster — depthBasedTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                  +
                                                  + + + + +
                                                  + +
                                                  +
                                                  +
                                                  +

                                                  Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster

                                                  + Source: R/Microclusters.R + +
                                                  + +
                                                  +

                                                  Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster

                                                  +
                                                  + + 
                                                  depthBasedTreeCluster(tree, target = 10)
                                                  + +

                                                  Arguments

                                                  + + + + + + + + + + +
                                                  tree

                                                  object of class phylo

                                                  target

                                                  number of clusters to attempt to generate

                                                  + +

                                                  Value

                                                  + +

                                                  List of clusters, each entry being a vector of indices representing +samples in the cluster.

                                                  + +
                                                  + +
                                                  + + +
                                                  +
                                                  +

                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                  +
                                                  + +
                                                  +

                                                  Site built with pkgdown 1.6.1.

                                                  +
                                                  + +
                                                  +
                                                  + + + + + + + + diff --git a/docs/reference/dot-colNormHelper.html b/docs/reference/dot-colNormHelper.html index b4cfead3..5d5b6423 100644 --- a/docs/reference/dot-colNormHelper.html +++ b/docs/reference/dot-colNormHelper.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                  • - +
                                                    • @@ -116,6 +116,12 @@
                                                  • Incorporating a Trajectory Model
                                                    • +
                                                  • + PhyloVision and Hotspot +
                                                    • +
                                                  • + Spatial Data and Hotspot +
                                                  • How To: Working with Seurat
                                                    • @@ -134,7 +140,7 @@
                                                    • - +
                                                      • @@ -160,7 +166,7 @@

                                                      Calculates the column znormalization after row znormalization

                                                      Helper to do this without inflating the matrix

                                                      - 
                                                      .colNormHelper(data, rowOffsets, rowScaleFactors)
                                                      + 
                                                      .colNormHelper(data, rowOffsets, rowScaleFactors)

                                                      Arguments

                                                      @@ -194,11 +200,11 @@

                                                      Contents

                                                      -

                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                      +

                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                      -

                                                      Site built with pkgdown 1.5.1.

                                                      +

                                                      Site built with pkgdown 1.6.1.

                                                      diff --git a/docs/reference/draw_hotspot_heatmap.html b/docs/reference/draw_hotspot_heatmap.html new file mode 100644 index 00000000..6c8475bf --- /dev/null +++ b/docs/reference/draw_hotspot_heatmap.html @@ -0,0 +1,212 @@ + + + + + + + + +Draw Modules Heatmap (Gene x Gene) — draw_hotspot_heatmap • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                      +
                                                      + + + + +
                                                      + +
                                                      +
                                                      +
                                                      +

                                                      Draw Modules Heatmap (Gene x Gene)

                                                      + Source: R/methods-Module.R + +
                                                      + +
                                                      +

                                                      Draw Modules Heatmap (Gene x Gene)

                                                      +
                                                      + + 
                                                      draw_hotspot_heatmap(hs, palette = paletteer_d("ggsci::default_nejm"))
                                                      + +

                                                      Arguments

                                                      +
                                                      + + + + + + + + + +
                                                      hs

                                                      the Hotspot Object

                                                      palette

                                                      palette

                                                      + + + + + + + +
                                                      +
                                                      +

                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                      +
                                                      + +
                                                      +

                                                      Site built with pkgdown 1.6.1.

                                                      +
                                                      + +
                                                      + + + + + + + + + diff --git a/docs/reference/evalSigGeneImportance.html b/docs/reference/evalSigGeneImportance.html index d97740c6..914f1f3a 100644 --- a/docs/reference/evalSigGeneImportance.html +++ b/docs/reference/evalSigGeneImportance.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 @@ -92,7 +92,7 @@
                                                      • - +
                                                        • @@ -118,6 +118,12 @@
                                                      • Incorporating a Trajectory Model
                                                        • +
                                                      • + PhyloVision and Hotspot +
                                                        • +
                                                      • + Spatial Data and Hotspot +
                                                      • How To: Working with Seurat
                                                        • @@ -136,7 +142,7 @@
                                                        • - +
                                                          • @@ -164,7 +170,7 @@

                                                          Calculate gene-signature importance

                                                          The correlation of genes with a negative sign in the signature are inverted.

                                                          - 
                                                          evalSigGeneImportance(sigScores, sigData, normExpr)
                                                          + 
                                                          evalSigGeneImportance(sigScores, sigData, normExpr)

                                                          Arguments

                                                          @@ -199,11 +205,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/evalSigGeneImportanceSparse.html b/docs/reference/evalSigGeneImportanceSparse.html index 1f3685a8..466f0767 100644 --- a/docs/reference/evalSigGeneImportanceSparse.html +++ b/docs/reference/evalSigGeneImportanceSparse.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 @@ -92,7 +92,7 @@
                                                          @@ -207,11 +213,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/fbConsistencyScores.html b/docs/reference/fbConsistencyScores.html index 5bcd482e..cd99feed 100644 --- a/docs/reference/fbConsistencyScores.html +++ b/docs/reference/fbConsistencyScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                          @@ -191,11 +197,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/filterGenesFano.html b/docs/reference/filterGenesFano.html index 5ead853c..abc2cd16 100644 --- a/docs/reference/filterGenesFano.html +++ b/docs/reference/filterGenesFano.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                          @@ -194,11 +200,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/filterGenesNovar.html b/docs/reference/filterGenesNovar.html index 22918355..58910f2f 100644 --- a/docs/reference/filterGenesNovar.html +++ b/docs/reference/filterGenesNovar.html @@ -88,7 +88,7 @@ VISION - 2.1.0 + 3.0.0 @@ -96,7 +96,7 @@
                                                          @@ -196,11 +202,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/filterGenesThreshold.html b/docs/reference/filterGenesThreshold.html index c563c8f7..cb19270a 100644 --- a/docs/reference/filterGenesThreshold.html +++ b/docs/reference/filterGenesThreshold.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                          @@ -190,11 +196,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/find_knn_parallel.html b/docs/reference/find_knn_parallel.html index ef2728be..eb3b2452 100644 --- a/docs/reference/find_knn_parallel.html +++ b/docs/reference/find_knn_parallel.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 @@ -92,7 +92,7 @@
                                                          @@ -196,11 +202,11 @@

                                                          Contents

                                                          -

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          -

                                                          Site built with pkgdown 1.5.1.

                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          diff --git a/docs/reference/find_knn_parallel_tree.html b/docs/reference/find_knn_parallel_tree.html new file mode 100644 index 00000000..81c839e2 --- /dev/null +++ b/docs/reference/find_knn_parallel_tree.html @@ -0,0 +1,221 @@ + + + + + + + + +Parallel KNN for Trees — find_knn_parallel_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                          +
                                                          + + + + +
                                                          + +
                                                          +
                                                          +
                                                          +

                                                          Parallel KNN for Trees

                                                          + Source: R/Utilities.R + +
                                                          + +
                                                          +

                                                          Computes nearest-neighbor indices and distances +in parallel. Query is over all points and results +do not include the self-distance.

                                                          +
                                                          + + 
                                                          find_knn_parallel_tree(tree, K)
                                                          + +

                                                          Arguments

                                                          +
                                                          + + + + + + + + + +
                                                          tree

                                                          an object of class phylo

                                                          K

                                                          number of neighbors to query

                                                          + +

                                                          Value

                                                          + +

                                                          list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances

                                                          + + + + + + +
                                                          +
                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          +
                                                          + +
                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          +
                                                          + +
                                                          + + + + + + + + + diff --git a/docs/reference/find_root.html b/docs/reference/find_root.html new file mode 100644 index 00000000..b057e4e3 --- /dev/null +++ b/docs/reference/find_root.html @@ -0,0 +1,211 @@ + + + + + + + + +Find the root node — find_root • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                          +
                                                          + + + + +
                                                          + +
                                                          +
                                                          +
                                                          +

                                                          Find the root node

                                                          + Source: R/Utilities.R + +
                                                          + +
                                                          +

                                                          Find the root node

                                                          +
                                                          + + 
                                                          find_root(tree)
                                                          + +

                                                          Arguments

                                                          + + + + + + +
                                                          tree

                                                          an object of class phylo

                                                          + +

                                                          Value

                                                          + +

                                                          the index of the root node

                                                          + +
                                                          + +
                                                          + + +
                                                          +
                                                          +

                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                          +
                                                          + +
                                                          +

                                                          Site built with pkgdown 1.6.1.

                                                          +
                                                          + +
                                                          +
                                                          + + + + + + + + diff --git a/docs/reference/fitTree.html b/docs/reference/fitTree.html index 8b6b1fff..95a63543 100644 --- a/docs/reference/fitTree.html +++ b/docs/reference/fitTree.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                          • - +
                                                            • @@ -116,6 +116,12 @@
                                                          • Incorporating a Trajectory Model
                                                            • +
                                                          • + PhyloVision and Hotspot +
                                                            • +
                                                          • + Spatial Data and Hotspot +
                                                          • How To: Working with Seurat
                                                            • @@ -134,7 +140,7 @@
                                                            • - +
                                                              • @@ -160,7 +166,7 @@

                                                              Fit tree using input parameters

                                                              Fit tree using input parameters

                                                              - 
                                                              fitTree(expr, nNodes, sigma, gamma, tol, maxIter)
                                                              + 
                                                              fitTree(expr, nNodes, sigma, gamma, tol, maxIter)

                                                              Arguments

                                                              @@ -213,11 +219,11 @@

                                                              Contents

                                                              -

                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                              +

                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                              -

                                                              Site built with pkgdown 1.5.1.

                                                              +

                                                              Site built with pkgdown 1.6.1.

                                                              diff --git a/docs/reference/geary_sig_v_proj.html b/docs/reference/geary_sig_v_proj.html index ca1f7cfd..dd74bb23 100644 --- a/docs/reference/geary_sig_v_proj.html +++ b/docs/reference/geary_sig_v_proj.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                              @@ -195,11 +201,11 @@

                                                              Contents

                                                              -

                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                              +

                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                              -

                                                              Site built with pkgdown 1.5.1.

                                                              +

                                                              Site built with pkgdown 1.6.1.

                                                              diff --git a/docs/reference/generateOverlapSignatures.html b/docs/reference/generateOverlapSignatures.html new file mode 100644 index 00000000..d2b5fe8f --- /dev/null +++ b/docs/reference/generateOverlapSignatures.html @@ -0,0 +1,211 @@ + + + + + + + + +Generates signature objects for the overlap sets between modules and signatures — generateOverlapSignatures • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                              +
                                                              + + + + +
                                                              + +
                                                              +
                                                              +
                                                              +

                                                              Generates signature objects for the overlap sets between modules and signatures

                                                              + Source: R/methods-Module.R + +
                                                              + +
                                                              +

                                                              Generates signature objects for the overlap sets between modules and signatures

                                                              +
                                                              + + 
                                                              generateOverlapSignatures(object)
                                                              + +

                                                              Arguments

                                                              +
                                                              + + + + + +
                                                              object

                                                              the Vision object

                                                              + +

                                                              Value

                                                              + +

                                                              Vision Object, populates the modData slot with overlap signatures.

                                                              + + + + + + +
                                                              +
                                                              +

                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                              +
                                                              + +
                                                              +

                                                              Site built with pkgdown 1.6.1.

                                                              +
                                                              + +
                                                              + + + + + + + + + diff --git a/docs/reference/generatePermutationNull.html b/docs/reference/generatePermutationNull.html index 762ed737..a7112f94 100644 --- a/docs/reference/generatePermutationNull.html +++ b/docs/reference/generatePermutationNull.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                              • - +
                                                                • @@ -116,6 +116,12 @@
                                                              • Incorporating a Trajectory Model
                                                                • +
                                                              • + PhyloVision and Hotspot +
                                                                • +
                                                              • + Spatial Data and Hotspot +
                                                              • How To: Working with Seurat
                                                                • @@ -134,7 +140,7 @@
                                                                • - +
                                                                  • @@ -160,7 +166,7 @@

                                                                  Generate random signatures for a null distribution by permuting the data

                                                                  Generate random signatures for a null distribution by permuting the data

                                                                  - 
                                                                  generatePermutationNull(eData, sigData, num)
                                                                  + 
                                                                  generatePermutationNull(eData, sigData, num)

                                                                  Arguments

                                                                  @@ -199,11 +205,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/generateProjections.html b/docs/reference/generateProjections.html index 862b3c06..231091c8 100644 --- a/docs/reference/generateProjections.html +++ b/docs/reference/generateProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -188,11 +194,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/generateProjectionsInner.html b/docs/reference/generateProjectionsInner.html index 60ef812f..ce04fdd7 100644 --- a/docs/reference/generateProjectionsInner.html +++ b/docs/reference/generateProjectionsInner.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -208,11 +214,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/generateTrajectoryProjections.html b/docs/reference/generateTrajectoryProjections.html index 22849658..4e3a004d 100644 --- a/docs/reference/generateTrajectoryProjections.html +++ b/docs/reference/generateTrajectoryProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -188,11 +194,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getLatentSpace.html b/docs/reference/getLatentSpace.html index 8a54d3ad..924ee5d2 100644 --- a/docs/reference/getLatentSpace.html +++ b/docs/reference/getLatentSpace.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -193,11 +199,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getLatentTrajectory.html b/docs/reference/getLatentTrajectory.html index 62976cbb..9d77f033 100644 --- a/docs/reference/getLatentTrajectory.html +++ b/docs/reference/getLatentTrajectory.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -183,12 +189,12 @@

                                                                  Details instead

                                                                  Examples

                                                                  - 
                                                                  if (FALSE) {
+    
                                                                  if (FALSE) {
 
-trajectory <- getLatentTrajectory(vis)
+trajectory <- getLatentTrajectory(vis)
 
 # MxM connectivity for network milestones
-trajectory@adjMat
+trajectory@adjMat
 
 # data.frame with the position of cells between milestones
 # Columns are:
@@ -196,9 +202,10 @@ 
                                                                  Examp
 #    from (milestone)
 #    to (milestone)
 #    position (0 to 1)
-trajectory@progressions
+trajectory@progressions
 
-}
                                                                  
+}
+
                                                                  @@ -90,7 +90,7 @@
                                                                  @@ -190,11 +196,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getMetaAutocorrelation.html b/docs/reference/getMetaAutocorrelation.html index 24b95106..09e64eb6 100644 --- a/docs/reference/getMetaAutocorrelation.html +++ b/docs/reference/getMetaAutocorrelation.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -191,11 +197,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getMetaDifferential.html b/docs/reference/getMetaDifferential.html index d9b4b576..40f53f01 100644 --- a/docs/reference/getMetaDifferential.html +++ b/docs/reference/getMetaDifferential.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -196,11 +202,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getNormalizedCopy.html b/docs/reference/getNormalizedCopy.html index 7d09cc66..3a14d18b 100644 --- a/docs/reference/getNormalizedCopy.html +++ b/docs/reference/getNormalizedCopy.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -190,11 +196,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getNormalizedCopySparse.html b/docs/reference/getNormalizedCopySparse.html index 9a9c48dd..a8589bf1 100644 --- a/docs/reference/getNormalizedCopySparse.html +++ b/docs/reference/getNormalizedCopySparse.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -190,11 +196,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html index 94757c5e..25963625 100644 --- a/docs/reference/getParam.html +++ b/docs/reference/getParam.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -194,11 +200,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getProjections.html b/docs/reference/getProjections.html index 6f34c0f5..97d93b8d 100644 --- a/docs/reference/getProjections.html +++ b/docs/reference/getProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -179,20 +185,21 @@

                                                                  Value

                                                                  List of matrix (Cells x 2)

                                                                  Examples

                                                                  - 
                                                                  if (FALSE) {
+    
                                                                  if (FALSE) {
 
 # After running 'analyze'
 # Retrieve tSNE30 (tSNE with perplexity 30) and plot it
 
-tsne <- getProjections(vis)[["tSNE30"]]
+tsne <- getProjections(vis)[["tSNE30"]]
 
-plot(tsne[, 1], tsne[, 2])
+plot(tsne[, 1], tsne[, 2])
 
 # To see the names of available projections, just run:
 
-names(getProjections(vis))
+names(getProjections(vis))
 
-}
                                                                  
+}
+
                                                                  @@ -90,7 +90,7 @@
                                                                  @@ -180,18 +186,19 @@

                                                                  Details

                                                                  This method allows you to retrieve saved selections later in R for downstream analyses

                                                                  Note: In order for selections to correctly save when launching the report, the report must be run by storing the results back into the object.

                                                                  -

                                                                  E.g.

                                                                  vis &lt;- viewResults(vis)

                                                                  and not

                                                                  viewResults(vis)
                                                                  +

                                                                  E.g.

                                                                  vis <- viewResults(vis)

                                                                  and not

                                                                  viewResults(vis)

                                                                  Examples

                                                                  - 
                                                                  if (FALSE) {
+    
                                                                  if (FALSE) {
 
-vis <- viewResults(vis)  # Selections saved while viewing results
+vis <- viewResults(vis)  # Selections saved while viewing results
 
 # Retrieve cell IDs for a selection group named 'interesting cells'
-interestingCells <- getSelections(vis)[['interesting cells']]
+interestingCells <- getSelections(vis)[['interesting cells']]
 
-}
                                                                  
+}
+
                                                                  @@ -90,7 +90,7 @@
                                                                  @@ -191,11 +197,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getSignatureDifferential.html b/docs/reference/getSignatureDifferential.html index 27c697e5..94988765 100644 --- a/docs/reference/getSignatureDifferential.html +++ b/docs/reference/getSignatureDifferential.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                  @@ -195,11 +201,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/getSignatureScores.html b/docs/reference/getSignatureScores.html index 193e871d..609ef0c5 100644 --- a/docs/reference/getSignatureScores.html +++ b/docs/reference/getSignatureScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  @@ -187,11 +193,11 @@

                                                                  Contents

                                                                  -

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  -

                                                                  Site built with pkgdown 1.5.1.

                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  diff --git a/docs/reference/get_all_children.html b/docs/reference/get_all_children.html new file mode 100644 index 00000000..c9b5b8f5 --- /dev/null +++ b/docs/reference/get_all_children.html @@ -0,0 +1,215 @@ + + + + + + + + +Get all the tip children of a node. — get_all_children • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Get all the tip children of a node.

                                                                  + Source: R/Utilities.R + +
                                                                  + +
                                                                  +

                                                                  Get all the tip children of a node.

                                                                  +
                                                                  + + 
                                                                  get_all_children(tree, node)
                                                                  + +

                                                                  Arguments

                                                                  +
                                                                  + + + + + + + + + +
                                                                  tree

                                                                  an object of class phylo

                                                                  node

                                                                  the node to check

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  the tips

                                                                  + + + + + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  + + + + + + + + + diff --git a/docs/reference/get_children.html b/docs/reference/get_children.html new file mode 100644 index 00000000..d67de3bc --- /dev/null +++ b/docs/reference/get_children.html @@ -0,0 +1,215 @@ + + + + + + + + +Find the children of a node — get_children • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Find the children of a node

                                                                  + Source: R/Utilities.R + +
                                                                  + +
                                                                  +

                                                                  Find the children of a node

                                                                  +
                                                                  + + 
                                                                  get_children(tree, node)
                                                                  + +

                                                                  Arguments

                                                                  + + + + + + + + + + +
                                                                  tree

                                                                  an object of class phylo

                                                                  node

                                                                  the node to get the children of

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  the children

                                                                  + +
                                                                  + +
                                                                  + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  +
                                                                  + + + + + + + + diff --git a/docs/reference/get_max_cluster_size.html b/docs/reference/get_max_cluster_size.html new file mode 100644 index 00000000..8a351371 --- /dev/null +++ b/docs/reference/get_max_cluster_size.html @@ -0,0 +1,215 @@ + + + + + + + + +Tree method for getting the max child clade size of a node — get_max_cluster_size • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Tree method for getting the max child clade size of a node

                                                                  + Source: R/Utilities.R + +
                                                                  + +
                                                                  +

                                                                  Tree method for getting the max child clade size of a node

                                                                  +
                                                                  + + 
                                                                  get_max_cluster_size(tree, node)
                                                                  + +

                                                                  Arguments

                                                                  + + + + + + + + + + +
                                                                  tree

                                                                  an object of class phylo

                                                                  node

                                                                  the node to check

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  the size of the largest child clade

                                                                  + +
                                                                  + +
                                                                  + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  +
                                                                  + + + + + + + + diff --git a/docs/reference/get_min_cluster_size.html b/docs/reference/get_min_cluster_size.html new file mode 100644 index 00000000..2f40b233 --- /dev/null +++ b/docs/reference/get_min_cluster_size.html @@ -0,0 +1,215 @@ + + + + + + + + +Tree method for getting the min child clade size of a node — get_min_cluster_size • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Tree method for getting the min child clade size of a node

                                                                  + Source: R/Utilities.R + +
                                                                  + +
                                                                  +

                                                                  Tree method for getting the min child clade size of a node

                                                                  +
                                                                  + + 
                                                                  get_min_cluster_size(tree, node)
                                                                  + +

                                                                  Arguments

                                                                  + + + + + + + + + + +
                                                                  tree

                                                                  an object of class phylo

                                                                  node

                                                                  the node to check

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  the size of the smallest child clade

                                                                  + +
                                                                  + +
                                                                  + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  +
                                                                  + + + + + + + + diff --git a/docs/reference/get_parent.html b/docs/reference/get_parent.html new file mode 100644 index 00000000..a3d45b3d --- /dev/null +++ b/docs/reference/get_parent.html @@ -0,0 +1,215 @@ + + + + + + + + +Get the parent of a node — get_parent • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Get the parent of a node

                                                                  + Source: R/Utilities.R + +
                                                                  + +
                                                                  +

                                                                  Get the parent of a node

                                                                  +
                                                                  + + 
                                                                  get_parent(tree, node)
                                                                  + +

                                                                  Arguments

                                                                  + + + + + + + + + + +
                                                                  tree

                                                                  an object of class phylo

                                                                  node

                                                                  the node to get parent

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  the immediate parent of the mode, or the node if it is root

                                                                  + +
                                                                  + +
                                                                  + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  +
                                                                  + + + + + + + + diff --git a/docs/reference/group_modules_enrichment.html b/docs/reference/group_modules_enrichment.html new file mode 100644 index 00000000..f899f5e4 --- /dev/null +++ b/docs/reference/group_modules_enrichment.html @@ -0,0 +1,225 @@ + + + + + + + + +Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table. — group_modules_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                  +
                                                                  + + + + +
                                                                  + +
                                                                  +
                                                                  +
                                                                  +

                                                                  Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table.

                                                                  + Source: R/methods-Module.R + +
                                                                  + +
                                                                  +

                                                                  Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table.

                                                                  +
                                                                  + + 
                                                                  group_modules_enrichment(stats, pvals)
                                                                  + +

                                                                  Arguments

                                                                  + + + + + + + + + + +
                                                                  stats

                                                                  overlap stats from calc_set_enrichment

                                                                  pvals

                                                                  overlap p values from calc_set_enrichment

                                                                  + +

                                                                  Value

                                                                  + +

                                                                  assignments of each signature to each module

                                                                  + +
                                                                  + +
                                                                  + + +
                                                                  +
                                                                  +

                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                  +
                                                                  + +
                                                                  +

                                                                  Site built with pkgdown 1.6.1.

                                                                  +
                                                                  + +
                                                                  +
                                                                  + + + + + + + + diff --git a/docs/reference/hasUnnormalizedData.html b/docs/reference/hasUnnormalizedData.html index abe79387..bf2a0fe5 100644 --- a/docs/reference/hasUnnormalizedData.html +++ b/docs/reference/hasUnnormalizedData.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                  • - +
                                                                    • @@ -116,6 +116,12 @@
                                                                  • Incorporating a Trajectory Model
                                                                    • +
                                                                  • + PhyloVision and Hotspot +
                                                                    • +
                                                                  • + Spatial Data and Hotspot +
                                                                  • How To: Working with Seurat
                                                                    • @@ -134,7 +140,7 @@
                                                                    • - +
                                                                      • @@ -160,7 +166,7 @@

                                                                      Tests for Unnormalized Data

                                                                      Determines if the VISION object is storing unnormalized data

                                                                      - 
                                                                      hasUnnormalizedData(object)
                                                                      + 
                                                                      hasUnnormalizedData(object)

                                                                      Arguments

                                                                      @@ -186,11 +192,11 @@

                                                                      Contents

                                                                      -

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      -

                                                                      Site built with pkgdown 1.5.1.

                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      diff --git a/docs/reference/hsCalculateModuleScores.html b/docs/reference/hsCalculateModuleScores.html new file mode 100644 index 00000000..bdbbf898 --- /dev/null +++ b/docs/reference/hsCalculateModuleScores.html @@ -0,0 +1,229 @@ + + + + + + + + +Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated — hsCalculateModuleScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                      +
                                                                      + + + + +
                                                                      + +
                                                                      +
                                                                      +
                                                                      +

                                                                      Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

                                                                      + Source: R/methods-Module.R + +
                                                                      + +
                                                                      +

                                                                      Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

                                                                      +
                                                                      + + 
                                                                      hsCalculateModuleScores(
+  hs,
+  min_gene_threshold = 20,
+  clustering_fdr = 0.5,
+  plot = F
+)
                                                                      + +

                                                                      Arguments

                                                                      +
                                                                      + + + + + + + + + + + + + +
                                                                      hs

                                                                      the Hotspot object, must have ran compute_local_correlations already

                                                                      min_gene_threshold

                                                                      min genes per module

                                                                      clustering_fdr

                                                                      p value for clustering genes

                                                                      + +

                                                                      Value

                                                                      + +

                                                                      the modified hs object

                                                                      + + + + + + +
                                                                      +
                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      +
                                                                      + +
                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      +
                                                                      + +
                                                                      + + + + + + + + + diff --git a/docs/reference/hsComputeAutoCorrelations.html b/docs/reference/hsComputeAutoCorrelations.html new file mode 100644 index 00000000..76475339 --- /dev/null +++ b/docs/reference/hsComputeAutoCorrelations.html @@ -0,0 +1,223 @@ + + + + + + + + +Compute Hotspot auto correlations — hsComputeAutoCorrelations • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                      +
                                                                      + + + + +
                                                                      + +
                                                                      +
                                                                      +
                                                                      +

                                                                      Compute Hotspot auto correlations

                                                                      + Source: R/methods-Module.R + +
                                                                      + +
                                                                      +

                                                                      Compute Hotspot auto correlations

                                                                      +
                                                                      + + 
                                                                      hsComputeAutoCorrelations(
+  hs,
+  number_top_genes = 1000,
+  autocorrelation_fdr = 0.05
+)
                                                                      + +

                                                                      Arguments

                                                                      + + + + + + + + + + + + + + +
                                                                      hs

                                                                      the Hotspot object

                                                                      number_top_genes

                                                                      Hotspot argument for number of genes to consider

                                                                      autocorrelation_fdr

                                                                      threshold for significance for genes autocorr

                                                                      + +

                                                                      Value

                                                                      + +

                                                                      list of HS genes

                                                                      + +
                                                                      + +
                                                                      + + +
                                                                      +
                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      +
                                                                      + +
                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      +
                                                                      + +
                                                                      +
                                                                      + + + + + + + + diff --git a/docs/reference/hsComputeLocalCorrelations.html b/docs/reference/hsComputeLocalCorrelations.html new file mode 100644 index 00000000..a4c1bb55 --- /dev/null +++ b/docs/reference/hsComputeLocalCorrelations.html @@ -0,0 +1,220 @@ + + + + + + + + +Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument — hsComputeLocalCorrelations • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                      +
                                                                      + + + + +
                                                                      + +
                                                                      +
                                                                      +
                                                                      +

                                                                      Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

                                                                      + Source: R/methods-Module.R + +
                                                                      + +
                                                                      +

                                                                      Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

                                                                      +
                                                                      + + 
                                                                      hsComputeLocalCorrelations(hs, hs_genes)
                                                                      + +

                                                                      Arguments

                                                                      + + + + + + + + + + +
                                                                      hs

                                                                      the Hotspot object

                                                                      hs_genes

                                                                      Hotspot genes

                                                                      + +

                                                                      Value

                                                                      + +

                                                                      the populated hs object

                                                                      + +
                                                                      + +
                                                                      + + +
                                                                      +
                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      +
                                                                      + +
                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      +
                                                                      + +
                                                                      +
                                                                      + + + + + + + + diff --git a/docs/reference/hsCreateKnnGraph.html b/docs/reference/hsCreateKnnGraph.html new file mode 100644 index 00000000..b86d1257 --- /dev/null +++ b/docs/reference/hsCreateKnnGraph.html @@ -0,0 +1,203 @@ + + + + + + + + +Init KNN graph in Hotspot object — hsCreateKnnGraph • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                      +
                                                                      + + + + +
                                                                      + +
                                                                      +
                                                                      +
                                                                      +

                                                                      Init KNN graph in Hotspot object

                                                                      + Source: R/methods-Module.R + +
                                                                      + +
                                                                      +

                                                                      Init KNN graph in Hotspot object

                                                                      +
                                                                      + + 
                                                                      hsCreateKnnGraph(hs, object, n_neighbors = NULL)
                                                                      + + +

                                                                      Value

                                                                      + +

                                                                      the Hotspot object with KNN initialized

                                                                      + +
                                                                      + +
                                                                      + + +
                                                                      +
                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      +
                                                                      + +
                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      +
                                                                      + +
                                                                      +
                                                                      + + + + + + + + diff --git a/docs/reference/hsInit.html b/docs/reference/hsInit.html new file mode 100644 index 00000000..55fe22d4 --- /dev/null +++ b/docs/reference/hsInit.html @@ -0,0 +1,227 @@ + + + + + + + + +Init Hotspot object from Vision Object — hsInit • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                      +
                                                                      + + + + +
                                                                      + +
                                                                      +
                                                                      +
                                                                      +

                                                                      Init Hotspot object from Vision Object

                                                                      + Source: R/methods-Module.R + +
                                                                      + +
                                                                      +

                                                                      Init Hotspot object from Vision Object

                                                                      +
                                                                      + + 
                                                                      hsInit(object, model = "normal", tree = F, num_umi = NULL, logdata = FALSE)
                                                                      + +

                                                                      Arguments

                                                                      + + + + + + + + + + + + + + + + + + + + + + +
                                                                      object

                                                                      the Vision Object

                                                                      model

                                                                      the model for Hotspot (ie "normal", "danb"...)

                                                                      tree

                                                                      boolean, whether to use the tree as ls

                                                                      num_umi

                                                                      df of barcodes x num_umi

                                                                      logdata

                                                                      boolean, log the expression data, avoid for danb

                                                                      + +

                                                                      Value

                                                                      + +

                                                                      the Hotspot object

                                                                      + +
                                                                      + +
                                                                      + + +
                                                                      +
                                                                      +

                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                      +
                                                                      + +
                                                                      +

                                                                      Site built with pkgdown 1.6.1.

                                                                      +
                                                                      + +
                                                                      +
                                                                      + + + + + + + + diff --git a/docs/reference/ilog1p.html b/docs/reference/ilog1p.html index 1473b053..6b76ac9c 100644 --- a/docs/reference/ilog1p.html +++ b/docs/reference/ilog1p.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                      • - +
                                                                        • @@ -117,6 +117,12 @@
                                                                      • Incorporating a Trajectory Model
                                                                        • +
                                                                      • + PhyloVision and Hotspot +
                                                                        • +
                                                                      • + Spatial Data and Hotspot +
                                                                      • How To: Working with Seurat
                                                                        • @@ -135,7 +141,7 @@
                                                                        • - +
                                                                          • @@ -162,7 +168,7 @@

                                                                          inverse log-scale transform a dense OR sparse matrix

                                                                          operating on sparse matrices

                                                                          - 
                                                                          ilog1p(spmat)
                                                                          + 
                                                                          ilog1p(spmat)

                                                                          Arguments

                                                                          @@ -191,11 +197,11 @@

                                                                          Contents

                                                                          -

                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                          +

                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                          -

                                                                          Site built with pkgdown 1.5.1.

                                                                          +

                                                                          Site built with pkgdown 1.6.1.

                                                                          diff --git a/docs/reference/index.html b/docs/reference/index.html index 6aa885c7..83b4001d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 @@ -89,7 +89,7 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                          Aggregate meta-data for cells in pools
                                                                          +

                                                                          PhyloVision

                                                                          +

                                                                          +
                                                                          +

                                                                          PhyloVision()

                                                                          +

                                                                          Initializes a new PhyloVision Object

                                                                          +

                                                                          phyloAnalyze(<PhyloVision>)

                                                                          +

                                                                          Analyze a PhyloVision object

                                                                          +

                                                                          Hotspot

                                                                          +

                                                                          +
                                                                          +

                                                                          runHotspot()

                                                                          +

                                                                          Perform Hotspot analysis on Vision Object

                                                                          +

                                                                          hsInit()

                                                                          +

                                                                          Init Hotspot object from Vision Object

                                                                          +

                                                                          hsCreateKnnGraph()

                                                                          +

                                                                          Init KNN graph in Hotspot object

                                                                          +

                                                                          hsComputeAutoCorrelations()

                                                                          +

                                                                          Compute Hotspot auto correlations

                                                                          +

                                                                          hsComputeLocalCorrelations()

                                                                          +

                                                                          Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

                                                                          +

                                                                          hsCalculateModuleScores()

                                                                          +

                                                                          Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

                                                                          +

                                                                          analyzeHotspotObjectVision()

                                                                          +

                                                                          Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work.

                                                                          +

                                                                          loadHotspotObject()

                                                                          +

                                                                          Load in an existing Hotspot object from bytes or a file

                                                                          +

                                                                          draw_hotspot_heatmap()

                                                                          +

                                                                          Draw Modules Heatmap (Gene x Gene)
                                                                          @@ -366,11 +468,11 @@

                                                                          Contents

                                                                          -

                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                          +

                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                          -

                                                                          Site built with pkgdown 1.5.1.

                                                                          +

                                                                          Site built with pkgdown 1.6.1.

                                                                          diff --git a/docs/reference/innerEvalSignatureBatchNorm.html b/docs/reference/innerEvalSignatureBatchNorm.html index ab32a546..0493c2f7 100644 --- a/docs/reference/innerEvalSignatureBatchNorm.html +++ b/docs/reference/innerEvalSignatureBatchNorm.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                          • - +
                                                                            • @@ -116,6 +116,12 @@
                                                                          • Incorporating a Trajectory Model
                                                                            • +
                                                                          • + PhyloVision and Hotspot +
                                                                            • +
                                                                          • + Spatial Data and Hotspot +
                                                                          • How To: Working with Seurat
                                                                            • @@ -134,7 +140,7 @@
                                                                            • - +
                                                                              • @@ -160,7 +166,7 @@

                                                                              Used in inner loop of batchSigEvalNorm

                                                                              Computes signature scores without inflating the genes/cells matrix

                                                                              - 
                                                                              innerEvalSignatureBatchNorm(normData, sigs)
                                                                              + 
                                                                              innerEvalSignatureBatchNorm(normData, sigs)

                                                                              Arguments

                                                                              @@ -190,11 +196,11 @@

                                                                              Contents

                                                                              -

                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                              +

                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                              -

                                                                              Site built with pkgdown 1.5.1.

                                                                              +

                                                                              Site built with pkgdown 1.6.1.

                                                                              diff --git a/docs/reference/is_tip.html b/docs/reference/is_tip.html new file mode 100644 index 00000000..fa9058fc --- /dev/null +++ b/docs/reference/is_tip.html @@ -0,0 +1,215 @@ + + + + + + + + +Check if a child is a tip — is_tip • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                              +
                                                                              + + + + +
                                                                              + +
                                                                              +
                                                                              +
                                                                              +

                                                                              Check if a child is a tip

                                                                              + Source: R/Utilities.R + +
                                                                              + +
                                                                              +

                                                                              Check if a child is a tip

                                                                              +
                                                                              + + 
                                                                              is_tip(tree, node)
                                                                              + +

                                                                              Arguments

                                                                              +
                                                                              + + + + + + + + + +
                                                                              tree

                                                                              an object of class phylo

                                                                              node

                                                                              the node to check

                                                                              + +

                                                                              Value

                                                                              + +

                                                                              true or false

                                                                              + + + + + + +
                                                                              +
                                                                              +

                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                              +
                                                                              + +
                                                                              +

                                                                              Site built with pkgdown 1.6.1.

                                                                              +
                                                                              + +
                                                                              + + + + + + + + + diff --git a/docs/reference/knn_tree.html b/docs/reference/knn_tree.html new file mode 100644 index 00000000..7a918929 --- /dev/null +++ b/docs/reference/knn_tree.html @@ -0,0 +1,225 @@ + + + + + + + + +Helper KNN Function for Trees — knn_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                              +
                                                                              + + + + +
                                                                              + +
                                                                              +
                                                                              +
                                                                              +

                                                                              Helper KNN Function for Trees

                                                                              + Source: R/Utilities.R + +
                                                                              + +
                                                                              +

                                                                              Computes nearest-neighbor indices and distances +in serial. Query is over all points and results +do not include the self-distance.

                                                                              +
                                                                              + + 
                                                                              knn_tree(leaves, k, distances)
                                                                              + +

                                                                              Arguments

                                                                              + + + + + + + + + + + + + + +
                                                                              leaves

                                                                              leaves to find the nearest neighbors of

                                                                              k

                                                                              number of neighbors to query

                                                                              distances

                                                                              matrix of Samples x Samples matrix of cophenetic tree distances

                                                                              + +

                                                                              Value

                                                                              + +

                                                                              list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances

                                                                              + +
                                                                              + +
                                                                              + + +
                                                                              +
                                                                              +

                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                              +
                                                                              + +
                                                                              +

                                                                              Site built with pkgdown 1.6.1.

                                                                              +
                                                                              + +
                                                                              +
                                                                              + + + + + + + + diff --git a/docs/reference/launchServer.html b/docs/reference/launchServer.html index dad2e80b..f3dea4d5 100644 --- a/docs/reference/launchServer.html +++ b/docs/reference/launchServer.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                              • - +
                                                                                • @@ -116,6 +116,12 @@
                                                                              • Incorporating a Trajectory Model
                                                                                • +
                                                                              • + PhyloVision and Hotspot +
                                                                                • +
                                                                              • + Spatial Data and Hotspot +
                                                                              • How To: Working with Seurat
                                                                                • @@ -134,7 +140,7 @@
                                                                                • - +
                                                                                  • @@ -160,7 +166,7 @@

                                                                                  Lanch the server

                                                                                  Lanch the server

                                                                                  - 
                                                                                  launchServer(object, port = NULL, host = NULL, browser = TRUE)
                                                                                  + 
                                                                                  launchServer(object, port = NULL, host = NULL, browser = TRUE)

                                                                                  Arguments

                                                                                  @@ -200,11 +206,11 @@

                                                                                  Contents

                                                                                  -

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                  +

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                  -

                                                                                  Site built with pkgdown 1.5.1.

                                                                                  +

                                                                                  Site built with pkgdown 1.6.1.

                                                                                  diff --git a/docs/reference/lcaBasedHotspotNeighbors.html b/docs/reference/lcaBasedHotspotNeighbors.html new file mode 100644 index 00000000..2edbc949 --- /dev/null +++ b/docs/reference/lcaBasedHotspotNeighbors.html @@ -0,0 +1,208 @@ + + + + + + + + +Add custom tree based neighbor and weights to a Hotspot object — lcaBasedHotspotNeighbors • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                  +
                                                                                  + + + + +
                                                                                  + +
                                                                                  +
                                                                                  +
                                                                                  +

                                                                                  Add custom tree based neighbor and weights to a Hotspot object

                                                                                  + Source: R/methods-Module.R + +
                                                                                  + +
                                                                                  +

                                                                                  @param tree object of class phylo + @param the Hotspot object to add the nw to + @param minSize the minimum number of neighbors of the node + @return the Hotspot object

                                                                                  +

                                                                                  @export

                                                                                  +
                                                                                  + + 
                                                                                  lcaBasedHotspotNeighbors(tree, hotspot, minSize = 20)
                                                                                  + + + +
                                                                                  + +
                                                                                  + + +
                                                                                  +
                                                                                  +

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                  +
                                                                                  + +
                                                                                  +

                                                                                  Site built with pkgdown 1.6.1.

                                                                                  +
                                                                                  + +
                                                                                  +
                                                                                  + + + + + + + + diff --git a/docs/reference/lcaBasedTreeKNN.html b/docs/reference/lcaBasedTreeKNN.html new file mode 100644 index 00000000..21fda540 --- /dev/null +++ b/docs/reference/lcaBasedTreeKNN.html @@ -0,0 +1,204 @@ + + + + + + + + +Generate neighbors and weights for a tree object, based on LCA. — lcaBasedTreeKNN • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                  +
                                                                                  + + + + +
                                                                                  + +
                                                                                  +
                                                                                  +
                                                                                  +

                                                                                  Generate neighbors and weights for a tree object, based on LCA.

                                                                                  + Source: R/Utilities.R + +
                                                                                  + +
                                                                                  +

                                                                                  @param tree object of class phylo + @param minSize the minimum number of neighbors per node + @return the hotspot object

                                                                                  +
                                                                                  + + 
                                                                                  lcaBasedTreeKNN(tree, minSize = 20)
                                                                                  + + + +
                                                                                  + +
                                                                                  + + +
                                                                                  +
                                                                                  +

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                  +
                                                                                  + +
                                                                                  +

                                                                                  Site built with pkgdown 1.6.1.

                                                                                  +
                                                                                  + +
                                                                                  +
                                                                                  + + + + + + + + diff --git a/docs/reference/lca_based_depth.html b/docs/reference/lca_based_depth.html new file mode 100644 index 00000000..a0986893 --- /dev/null +++ b/docs/reference/lca_based_depth.html @@ -0,0 +1,219 @@ + + + + + + + + +Depth of tip1 parent immediately after LCA(tip1, tip2) — lca_based_depth • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                  +
                                                                                  + + + + +
                                                                                  + +
                                                                                  +
                                                                                  +
                                                                                  +

                                                                                  Depth of tip1 parent immediately after LCA(tip1, tip2)

                                                                                  + Source: R/Utilities.R + +
                                                                                  + +
                                                                                  +

                                                                                  Depth of tip1 parent immediately after LCA(tip1, tip2)

                                                                                  +
                                                                                  + + 
                                                                                  lca_based_depth(tree, tip1, tip2)
                                                                                  + +

                                                                                  Arguments

                                                                                  +
                                                                                  + + + + + + + + + + + + + +
                                                                                  tree

                                                                                  an object of class phylo

                                                                                  tip1

                                                                                  the first leaf

                                                                                  tip2

                                                                                  the second leaf

                                                                                  + +

                                                                                  Value

                                                                                  + +

                                                                                  the trivial distance between tip1, tip2

                                                                                  + + + + + + +
                                                                                  +
                                                                                  +

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                  +
                                                                                  + +
                                                                                  +

                                                                                  Site built with pkgdown 1.6.1.

                                                                                  +
                                                                                  + +
                                                                                  + + + + + + + + + diff --git a/docs/reference/loadHotspotObject.html b/docs/reference/loadHotspotObject.html new file mode 100644 index 00000000..d2c6354e --- /dev/null +++ b/docs/reference/loadHotspotObject.html @@ -0,0 +1,215 @@ + + + + + + + + +Load in an existing Hotspot object from bytes or a file — loadHotspotObject • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                  +
                                                                                  + + + + +
                                                                                  + +
                                                                                  +
                                                                                  +
                                                                                  +

                                                                                  Load in an existing Hotspot object from bytes or a file

                                                                                  + Source: R/methods-Module.R + +
                                                                                  + +
                                                                                  +

                                                                                  Load in an existing Hotspot object from bytes or a file

                                                                                  +
                                                                                  + + 
                                                                                  loadHotspotObject(file = NULL, bytes = NULL)
                                                                                  + +

                                                                                  Arguments

                                                                                  + + + + + + + + + + +
                                                                                  file

                                                                                  optional path to an existing file containing pickled bytes (format 0)

                                                                                  bytes

                                                                                  optional R character vector of bytes created by calcHotspotModules

                                                                                  + +

                                                                                  Value

                                                                                  + +

                                                                                  an externalptr to a Hotspot Object loaded in the R reticulate session

                                                                                  + +
                                                                                  + +
                                                                                  + + +
                                                                                  +
                                                                                  +

                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                  +
                                                                                  + +
                                                                                  +

                                                                                  Site built with pkgdown 1.6.1.

                                                                                  +
                                                                                  + +
                                                                                  +
                                                                                  + + + + + + + + diff --git a/docs/reference/louvainCluster.html b/docs/reference/louvainCluster.html index 4b72ba73..c2fbe510 100644 --- a/docs/reference/louvainCluster.html +++ b/docs/reference/louvainCluster.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                  • - +
                                                                                    • @@ -116,6 +116,12 @@
                                                                                  • Incorporating a Trajectory Model
                                                                                    • +
                                                                                  • + PhyloVision and Hotspot +
                                                                                    • +
                                                                                  • + Spatial Data and Hotspot +
                                                                                  • How To: Working with Seurat
                                                                                    • @@ -134,7 +140,7 @@
                                                                                    • - +
                                                                                      • @@ -160,7 +166,7 @@

                                                                                      Applies the Louvain algorithm to generate micro-clustered data

                                                                                      Applies the Louvain algorithm to generate micro-clustered data

                                                                                      - 
                                                                                      louvainCluster(kn, data)
                                                                                      + 
                                                                                      louvainCluster(kn, data)

                                                                                      Arguments

                                                                                      @@ -192,11 +198,11 @@

                                                                                      Contents

                                                                                      -

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      -

                                                                                      Site built with pkgdown 1.5.1.

                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      diff --git a/docs/reference/matLog2.html b/docs/reference/matLog2.html index 45a297d9..e543bd3a 100644 --- a/docs/reference/matLog2.html +++ b/docs/reference/matLog2.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                      @@ -200,11 +206,11 @@

                                                                                      Contents

                                                                                      -

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      -

                                                                                      Site built with pkgdown 1.5.1.

                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      diff --git a/docs/reference/matrix_chisq.html b/docs/reference/matrix_chisq.html index e4b3cd63..98c360ee 100644 --- a/docs/reference/matrix_chisq.html +++ b/docs/reference/matrix_chisq.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                      @@ -193,11 +199,11 @@

                                                                                      Contents

                                                                                      -

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      -

                                                                                      Site built with pkgdown 1.5.1.

                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      diff --git a/docs/reference/matrix_wilcox.html b/docs/reference/matrix_wilcox.html index 1992f176..4bb4c074 100644 --- a/docs/reference/matrix_wilcox.html +++ b/docs/reference/matrix_wilcox.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                      @@ -201,11 +207,11 @@

                                                                                      Contents

                                                                                      -

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      -

                                                                                      Site built with pkgdown 1.5.1.

                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      diff --git a/docs/reference/matrix_wilcox_cpp.html b/docs/reference/matrix_wilcox_cpp.html index 4e2c126a..516ce506 100644 --- a/docs/reference/matrix_wilcox_cpp.html +++ b/docs/reference/matrix_wilcox_cpp.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                      @@ -210,11 +216,11 @@

                                                                                      Contents

                                                                                      -

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      -

                                                                                      Site built with pkgdown 1.5.1.

                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      diff --git a/docs/reference/maxSizeCladewiseTreeCluster.html b/docs/reference/maxSizeCladewiseTreeCluster.html new file mode 100644 index 00000000..bb9e70fa --- /dev/null +++ b/docs/reference/maxSizeCladewiseTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size — maxSizeCladewiseTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      +
                                                                                      + + + + +
                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size

                                                                                      + Source: R/Microclusters.R + +
                                                                                      + +
                                                                                      +

                                                                                      Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size

                                                                                      +
                                                                                      + + 
                                                                                      maxSizeCladewiseTreeCluster(tree, target = 10)
                                                                                      + +

                                                                                      Arguments

                                                                                      +
                                                                                      + + + + + + + + + +
                                                                                      tree

                                                                                      object of class phylo

                                                                                      target

                                                                                      number of clusters to attempt to generate

                                                                                      + +

                                                                                      Value

                                                                                      + +

                                                                                      List of clusters, each entry being a vector of tips representing +samples in the cluster.

                                                                                      + + + + + + +
                                                                                      +
                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      +
                                                                                      + +
                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      +
                                                                                      + +
                                                                                      + + + + + + + + + diff --git a/docs/reference/minSizeCladeNeighbors.html b/docs/reference/minSizeCladeNeighbors.html new file mode 100644 index 00000000..fd5eee86 --- /dev/null +++ b/docs/reference/minSizeCladeNeighbors.html @@ -0,0 +1,219 @@ + + + + + + + + +Get's the nearest >= min size neighbors of a node based on clade structure — minSizeCladeNeighbors • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                      +
                                                                                      + + + + +
                                                                                      + +
                                                                                      +
                                                                                      +
                                                                                      +

                                                                                      Get's the nearest >= min size neighbors of a node based on clade structure

                                                                                      + Source: R/Utilities.R + +
                                                                                      + +
                                                                                      +

                                                                                      Get's the nearest >= min size neighbors of a node based on clade structure

                                                                                      +
                                                                                      + + 
                                                                                      minSizeCladeNeighbors(tree, tip, minSize = 20)
                                                                                      + +

                                                                                      Arguments

                                                                                      + + + + + + + + + + + + + + +
                                                                                      tree

                                                                                      an object of class phylo

                                                                                      tip

                                                                                      the tip to find the neighbors of

                                                                                      minSize

                                                                                      the minimum number of neighbors of the node (excludes self)

                                                                                      + +

                                                                                      Value

                                                                                      + +

                                                                                      the neighbors

                                                                                      + +
                                                                                      + +
                                                                                      + + +
                                                                                      +
                                                                                      +

                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                      +
                                                                                      + +
                                                                                      +

                                                                                      Site built with pkgdown 1.6.1.

                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      + + + + + + + + diff --git a/docs/reference/noNormalization.html b/docs/reference/noNormalization.html index b5bdfc6d..3d0a38b4 100644 --- a/docs/reference/noNormalization.html +++ b/docs/reference/noNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                      • - +
                                                                                        • @@ -116,6 +116,12 @@
                                                                                      • Incorporating a Trajectory Model
                                                                                        • +
                                                                                      • + PhyloVision and Hotspot +
                                                                                        • +
                                                                                      • + Spatial Data and Hotspot +
                                                                                      • How To: Working with Seurat
                                                                                        • @@ -134,7 +140,7 @@
                                                                                        • - +
                                                                                          • @@ -160,7 +166,7 @@

                                                                                          Does nothing, just returns the original data

                                                                                          Does nothing, just returns the original data

                                                                                          - 
                                                                                          noNormalization(data)
                                                                                          + 
                                                                                          noNormalization(data)

                                                                                          Arguments

                                                                                          @@ -186,11 +192,11 @@

                                                                                          Contents

                                                                                          -

                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                          +

                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                          -

                                                                                          Site built with pkgdown 1.5.1.

                                                                                          +

                                                                                          Site built with pkgdown 1.6.1.

                                                                                          diff --git a/docs/reference/pearsonCorrToJSON.html b/docs/reference/pearsonCorrToJSON.html index 0d4e4b35..8686d1ba 100644 --- a/docs/reference/pearsonCorrToJSON.html +++ b/docs/reference/pearsonCorrToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                          @@ -190,11 +196,11 @@

                                                                                          Contents

                                                                                          -

                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                          +

                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                          -

                                                                                          Site built with pkgdown 1.5.1.

                                                                                          +

                                                                                          Site built with pkgdown 1.6.1.

                                                                                          diff --git a/docs/reference/phyloAnalyze-PhyloVision-method.html b/docs/reference/phyloAnalyze-PhyloVision-method.html new file mode 100644 index 00000000..8478a6dd --- /dev/null +++ b/docs/reference/phyloAnalyze-PhyloVision-method.html @@ -0,0 +1,209 @@ + + + + + + + + +Analyze a PhyloVision object — phyloAnalyze,PhyloVision-method • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                          +
                                                                                          + + + + +
                                                                                          + +
                                                                                          +
                                                                                          +
                                                                                          +

                                                                                          Analyze a PhyloVision object

                                                                                          + Source: R/methods-Vision.R + +
                                                                                          + +
                                                                                          +

                                                                                          Analyze a PhyloVision object

                                                                                          +
                                                                                          + + 
                                                                                          # S4 method for PhyloVision
+phyloAnalyze(object, hotspot = FALSE)
                                                                                          + +

                                                                                          Arguments

                                                                                          +
                                                                                          + + + + + +
                                                                                          ...

                                                                                          arguments passed to the base Vision constructor

                                                                                          + + + + + + + +
                                                                                          +
                                                                                          +

                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                          +
                                                                                          + +
                                                                                          +

                                                                                          Site built with pkgdown 1.6.1.

                                                                                          +
                                                                                          + +
                                                                                          + + + + + + + + + diff --git a/docs/reference/poolCells.html b/docs/reference/poolCells.html index 751be96f..802d4ff7 100644 --- a/docs/reference/poolCells.html +++ b/docs/reference/poolCells.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                                                                                          • - +
                                                                                            • @@ -119,6 +119,12 @@
                                                                                          • Incorporating a Trajectory Model
                                                                                            • +
                                                                                          • + PhyloVision and Hotspot +
                                                                                            • +
                                                                                          • + Spatial Data and Hotspot +
                                                                                          • How To: Working with Seurat
                                                                                            • @@ -137,7 +143,7 @@
                                                                                            • - +
                                                                                              • @@ -165,7 +171,7 @@

                                                                                              create micro-clusters that reduce noise and complexity while maintaining the overall signal in the data

                                                                                              - 
                                                                                              poolCells(object, cellsPerPartition = NULL)
                                                                                              + 
                                                                                              poolCells(object, cellsPerPartition = NULL)

                                                                                              Arguments

                                                                                              @@ -195,11 +201,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/poolMatrixCols.html b/docs/reference/poolMatrixCols.html index 6421dbdf..56212f90 100644 --- a/docs/reference/poolMatrixCols.html +++ b/docs/reference/poolMatrixCols.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -196,11 +202,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/poolMatrixCols_Inner.html b/docs/reference/poolMatrixCols_Inner.html index 64bb4d2a..3d9376a4 100644 --- a/docs/reference/poolMatrixCols_Inner.html +++ b/docs/reference/poolMatrixCols_Inner.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -190,11 +196,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/poolMatrixRows.html b/docs/reference/poolMatrixRows.html index 51b9a171..4ef56a0f 100644 --- a/docs/reference/poolMatrixRows.html +++ b/docs/reference/poolMatrixRows.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -195,11 +201,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/poolMetaData.html b/docs/reference/poolMetaData.html index 36d3cdd2..ebd89605 100644 --- a/docs/reference/poolMetaData.html +++ b/docs/reference/poolMetaData.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                              @@ -203,11 +209,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/processSignatures.html b/docs/reference/processSignatures.html index 71d57992..3ac716ea 100644 --- a/docs/reference/processSignatures.html +++ b/docs/reference/processSignatures.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                              @@ -202,11 +208,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/projectOnTree.html b/docs/reference/projectOnTree.html index 069da694..fdccb8ea 100644 --- a/docs/reference/projectOnTree.html +++ b/docs/reference/projectOnTree.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -206,11 +212,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/readSignaturesInput.html b/docs/reference/readSignaturesInput.html index 705d32d3..d0389658 100644 --- a/docs/reference/readSignaturesInput.html +++ b/docs/reference/readSignaturesInput.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -186,11 +192,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/read_10x.html b/docs/reference/read_10x.html index cd21025f..8abc359b 100644 --- a/docs/reference/read_10x.html +++ b/docs/reference/read_10x.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -210,11 +216,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/read_10x_h5.html b/docs/reference/read_10x_h5.html index 94f89e8a..d1c38754 100644 --- a/docs/reference/read_10x_h5.html +++ b/docs/reference/read_10x_h5.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -199,11 +205,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/read_10x_h5_v2.html b/docs/reference/read_10x_h5_v2.html index 1c74ba27..ab294a63 100644 --- a/docs/reference/read_10x_h5_v2.html +++ b/docs/reference/read_10x_h5_v2.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -195,11 +201,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/read_10x_h5_v3.html b/docs/reference/read_10x_h5_v3.html index 52452fba..0f2b5081 100644 --- a/docs/reference/read_10x_h5_v3.html +++ b/docs/reference/read_10x_h5_v3.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -197,11 +203,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/readjust_clusters.html b/docs/reference/readjust_clusters.html index 3d3094cd..1cdeb1a6 100644 --- a/docs/reference/readjust_clusters.html +++ b/docs/reference/readjust_clusters.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -91,7 +91,7 @@
                                                                                              @@ -200,11 +206,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/registerMethods.html b/docs/reference/registerMethods.html index 04dedf6a..7048b2d2 100644 --- a/docs/reference/registerMethods.html +++ b/docs/reference/registerMethods.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -190,11 +196,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/rowAndColNormalization.html b/docs/reference/rowAndColNormalization.html index 5b77d4cc..b2d5531d 100644 --- a/docs/reference/rowAndColNormalization.html +++ b/docs/reference/rowAndColNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -186,11 +192,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/rowNormalization.html b/docs/reference/rowNormalization.html index 97f2107b..a1e50c06 100644 --- a/docs/reference/rowNormalization.html +++ b/docs/reference/rowNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -186,11 +192,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/rowVarsSp.html b/docs/reference/rowVarsSp.html index ec24ccce..79cd9536 100644 --- a/docs/reference/rowVarsSp.html +++ b/docs/reference/rowVarsSp.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                              @@ -186,11 +192,11 @@

                                                                                              Contents

                                                                                              -

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              -

                                                                                              Site built with pkgdown 1.5.1.

                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              diff --git a/docs/reference/runHotspot.html b/docs/reference/runHotspot.html new file mode 100644 index 00000000..314a2bff --- /dev/null +++ b/docs/reference/runHotspot.html @@ -0,0 +1,268 @@ + + + + + + + + +Perform Hotspot analysis on Vision Object — runHotspot • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                              +
                                                                                              + + + + +
                                                                                              + +
                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Perform Hotspot analysis on Vision Object

                                                                                              + Source: R/methods-Module.R + +
                                                                                              + +
                                                                                              +

                                                                                              Perform Hotspot analysis on Vision Object

                                                                                              +
                                                                                              + + 
                                                                                              runHotspot(
+  object,
+  model = "normal",
+  tree = FALSE,
+  number_top_genes = 1000,
+  num_umi = NULL,
+  min_gene_threshold = 20,
+  n_neighbors = NULL,
+  autocorrelation_fdr = 0.05,
+  clustering_fdr = 0.5,
+  logdata = FALSE
+)
                                                                                              + +

                                                                                              Arguments

                                                                                              +
                                                                                              + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                              object

                                                                                              Vision Object

                                                                                              model

                                                                                              model argument for Hotspot, one of

                                                                                                +

                                                                                              • normal

                                                                                                • +

                                                                                              • danb

                                                                                                • +

                                                                                              • bernoulli

                                                                                                • +

                                                                                              • none

                                                                                                • +
                                                                                              tree

                                                                                              whether to use tree as latent space. If TRUE, object should have +a tree slot.

                                                                                              number_top_genes

                                                                                              Hotspot argument for number of genes to consider

                                                                                              num_umi

                                                                                              optional dataframe containing umi counts in first column for +barcodes

                                                                                              min_gene_threshold

                                                                                              minimum number of genes in Hotspot module

                                                                                              n_neighbors

                                                                                              number of neighbors to consider in latent space

                                                                                              autocorrelation_fdr

                                                                                              threshold for significance for genes autocorr

                                                                                              clustering_fdr

                                                                                              threshold for significance for clustering modules

                                                                                              logdata

                                                                                              boolean, log the expression data, avoid for danb +Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +and HotspotObject slots of object, as well as recalculates signature scores +for new modules.

                                                                                              + +

                                                                                              Value

                                                                                              + +

                                                                                              the modified Vision object

                                                                                              + + + + + + +
                                                                                              +
                                                                                              +

                                                                                              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                              +
                                                                                              + +
                                                                                              +

                                                                                              Site built with pkgdown 1.6.1.

                                                                                              +
                                                                                              + +
                                                                                              + + + + + + + + + diff --git a/docs/reference/saveAndViewResults-Vision-method.html b/docs/reference/saveAndViewResults-Vision-method.html index 8bf8bde6..ce9ef87c 100644 --- a/docs/reference/saveAndViewResults-Vision-method.html +++ b/docs/reference/saveAndViewResults-Vision-method.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 @@ -92,7 +92,7 @@
                                                                                              • - +
                                                                                                • @@ -118,6 +118,12 @@
                                                                                              • Incorporating a Trajectory Model
                                                                                                • +
                                                                                              • + PhyloVision and Hotspot +
                                                                                                • +
                                                                                              • + Spatial Data and Hotspot +
                                                                                              • How To: Working with Seurat
                                                                                                • @@ -136,7 +142,7 @@
                                                                                                • - +
                                                                                                  • @@ -164,14 +170,14 @@

                                                                                                  Save the VISION object as an .RDS file and view the results on a 
                                                                                                  # S4 method for Vision
-saveAndViewResults(
-  object,
-  ofile = NULL,
-  port = NULL,
-  host = NULL,
-  browser = TRUE,
-  name = NULL
-)
                                                                                                  +saveAndViewResults( + object, + ofile = NULL, + port = NULL, + host = NULL, + browser = TRUE, + name = NULL +)

                                                                                                  Arguments

                                                                                                  @@ -216,15 +222,16 @@

                                                                                                  Details viewResults(vis)

                                                                                                  Examples

                                                                                                  - 
                                                                                                  if (FALSE) {
+    
                                                                                                  if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-saveAndViewResults(vis, 'vision_results.rds') # Saves and launches dynamic output report
-}
                                                                                                  
+saveAndViewResults(vis, 'vision_results.rds') # Saves and launches dynamic output report
+}
+
                                                                                                  + + + + + + + + + +
                                                                                                  path

                                                                                                  the file path

                                                                                                  bytes

                                                                                                  the raw bytes, like in the Hotspot slot of a VISION Object

                                                                                                  + + + + + + + +
                                                                                                  +
                                                                                                  +

                                                                                                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                  +
                                                                                                  + +
                                                                                                  +

                                                                                                  Site built with pkgdown 1.6.1.

                                                                                                  +
                                                                                                  + +
                                                                                                  + + + + + + + + + diff --git a/docs/reference/sigConsistencyScores.html b/docs/reference/sigConsistencyScores.html index 93cc6f8f..50b4c5e7 100644 --- a/docs/reference/sigConsistencyScores.html +++ b/docs/reference/sigConsistencyScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                  • - +
                                                                                                    • @@ -116,6 +116,12 @@
                                                                                                  • Incorporating a Trajectory Model
                                                                                                    • +
                                                                                                  • + PhyloVision and Hotspot +
                                                                                                    • +
                                                                                                  • + Spatial Data and Hotspot +
                                                                                                  • How To: Working with Seurat
                                                                                                    • @@ -134,7 +140,7 @@
                                                                                                    • - +
                                                                                                      • @@ -160,7 +166,7 @@

                                                                                                      Evaluates the significance of each signature in each cluster

                                                                                                      Evaluates the significance of each signature in each cluster

                                                                                                      - 
                                                                                                      sigConsistencyScores(weights, sigScoresData, metaData, randomSigData, normExpr)
                                                                                                      + 
                                                                                                      sigConsistencyScores(weights, sigScoresData, metaData, randomSigData, normExpr)

                                                                                                      Arguments

                                                                                                      @@ -213,11 +219,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigProjMatrixToJSON.html b/docs/reference/sigProjMatrixToJSON.html index 7840182e..cea290b7 100644 --- a/docs/reference/sigProjMatrixToJSON.html +++ b/docs/reference/sigProjMatrixToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -194,11 +200,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigScoresToJSON.html b/docs/reference/sigScoresToJSON.html index bf664c5d..eabb12b6 100644 --- a/docs/reference/sigScoresToJSON.html +++ b/docs/reference/sigScoresToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -190,11 +196,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/signatureToJSON.html b/docs/reference/signatureToJSON.html index c3e5d14a..f2464339 100644 --- a/docs/reference/signatureToJSON.html +++ b/docs/reference/signatureToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -190,11 +196,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigsToSparseMatrix.html b/docs/reference/sigsToSparseMatrix.html index 7ba0115f..8cb220b8 100644 --- a/docs/reference/sigsToSparseMatrix.html +++ b/docs/reference/sigsToSparseMatrix.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -190,11 +196,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigsVsProjection_n.html b/docs/reference/sigsVsProjection_n.html index c51f2d58..df2480da 100644 --- a/docs/reference/sigsVsProjection_n.html +++ b/docs/reference/sigsVsProjection_n.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                                                                                                      @@ -222,11 +228,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigsVsProjection_pcf.html b/docs/reference/sigsVsProjection_pcf.html index 0146e4dc..be19a322 100644 --- a/docs/reference/sigsVsProjection_pcf.html +++ b/docs/reference/sigsVsProjection_pcf.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                                                                                                      @@ -204,11 +210,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sigsVsProjection_pcn.html b/docs/reference/sigsVsProjection_pcn.html index 20fbbd44..18419cd2 100644 --- a/docs/reference/sigsVsProjection_pcn.html +++ b/docs/reference/sigsVsProjection_pcn.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -93,7 +93,7 @@
                                                                                                      @@ -210,11 +216,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/sqdist.html b/docs/reference/sqdist.html index 81067c15..58032bb4 100644 --- a/docs/reference/sqdist.html +++ b/docs/reference/sqdist.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -190,11 +196,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/translateCellPositions.html b/docs/reference/translateCellPositions.html index 5fe375c9..541fa113 100644 --- a/docs/reference/translateCellPositions.html +++ b/docs/reference/translateCellPositions.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      @@ -194,11 +200,11 @@

                                                                                                      Contents

                                                                                                      -

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      -

                                                                                                      Site built with pkgdown 1.5.1.

                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      diff --git a/docs/reference/treeClusterMinCladeSize.html b/docs/reference/treeClusterMinCladeSize.html new file mode 100644 index 00000000..18085cfc --- /dev/null +++ b/docs/reference/treeClusterMinCladeSize.html @@ -0,0 +1,216 @@ + + + + + + + + +Generate clade-clusters for a tree of minimum size (unless children of root) — treeClusterMinCladeSize • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                                      +
                                                                                                      + + + + +
                                                                                                      + +
                                                                                                      +
                                                                                                      +
                                                                                                      +

                                                                                                      Generate clade-clusters for a tree of minimum size (unless children of root)

                                                                                                      + Source: R/Microclusters.R + +
                                                                                                      + +
                                                                                                      +

                                                                                                      Generate clade-clusters for a tree of minimum size (unless children of root)

                                                                                                      +
                                                                                                      + + 
                                                                                                      treeClusterMinCladeSize(tree, minSize = 30)
                                                                                                      + +

                                                                                                      Arguments

                                                                                                      +
                                                                                                      + + + + + + + + + +
                                                                                                      tree

                                                                                                      object of class phylo

                                                                                                      minSize

                                                                                                      minimum clade size for a clade to be expanded

                                                                                                      + +

                                                                                                      Value

                                                                                                      + +

                                                                                                      List of clusters, each entry being a vector of tips representing +WARNING: This won't work well for tree's with broad multifurcations

                                                                                                      + + + + + + +
                                                                                                      +
                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      +
                                                                                                      + +
                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      +
                                                                                                      + +
                                                                                                      + + + + + + + + + diff --git a/docs/reference/trivial_dist.html b/docs/reference/trivial_dist.html new file mode 100644 index 00000000..25f86a56 --- /dev/null +++ b/docs/reference/trivial_dist.html @@ -0,0 +1,221 @@ + + + + + + + + +Trivial distance function for arbitrary tree clustering — trivial_dist • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                                      +
                                                                                                      + + + + +
                                                                                                      + +
                                                                                                      +
                                                                                                      +
                                                                                                      +

                                                                                                      Trivial distance function for arbitrary tree clustering

                                                                                                      + Source: R/Utilities.R + +
                                                                                                      + +
                                                                                                      +

                                                                                                      Number of mutations along path from tip1 to LCA(tip1, tip2) +Ensures if on same clade, join.

                                                                                                      +
                                                                                                      + + 
                                                                                                      trivial_dist(tree, tip1, tip2)
                                                                                                      + +

                                                                                                      Arguments

                                                                                                      + + + + + + + + + + + + + + +
                                                                                                      tree

                                                                                                      an object of class phylo

                                                                                                      tip1

                                                                                                      the first leaf

                                                                                                      tip2

                                                                                                      the second leaf

                                                                                                      + +

                                                                                                      Value

                                                                                                      + +

                                                                                                      the trivial distance between tip1, tip2

                                                                                                      + +
                                                                                                      + +
                                                                                                      + + +
                                                                                                      +
                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      +
                                                                                                      + +
                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      +
                                                                                                      + +
                                                                                                      +
                                                                                                      + + + + + + + + diff --git a/docs/reference/ultrametric_tree.html b/docs/reference/ultrametric_tree.html new file mode 100644 index 00000000..ccc27f05 --- /dev/null +++ b/docs/reference/ultrametric_tree.html @@ -0,0 +1,211 @@ + + + + + + + + +Generate an ultrametric tree — ultrametric_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                                      +
                                                                                                      + + + + +
                                                                                                      + +
                                                                                                      +
                                                                                                      +
                                                                                                      +

                                                                                                      Generate an ultrametric tree

                                                                                                      + Source: R/Utilities.R + +
                                                                                                      + +
                                                                                                      +

                                                                                                      Generate an ultrametric tree

                                                                                                      +
                                                                                                      + + 
                                                                                                      ultrametric_tree(tree)
                                                                                                      + +

                                                                                                      Arguments

                                                                                                      + + + + + + +
                                                                                                      tree

                                                                                                      an object of class phylo

                                                                                                      + +

                                                                                                      Value

                                                                                                      + +

                                                                                                      a tree with edge distances such that it is ultrametric.

                                                                                                      + +
                                                                                                      + +
                                                                                                      + + +
                                                                                                      +
                                                                                                      +

                                                                                                      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                      +
                                                                                                      + +
                                                                                                      +

                                                                                                      Site built with pkgdown 1.6.1.

                                                                                                      +
                                                                                                      + +
                                                                                                      +
                                                                                                      + + + + + + + + diff --git a/docs/reference/versionCheck.html b/docs/reference/versionCheck.html index 5a2f0342..88e61294 100644 --- a/docs/reference/versionCheck.html +++ b/docs/reference/versionCheck.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                      • - +
                                                                                                        • @@ -116,6 +116,12 @@
                                                                                                      • Incorporating a Trajectory Model
                                                                                                        • +
                                                                                                      • + PhyloVision and Hotspot +
                                                                                                        • +
                                                                                                      • + Spatial Data and Hotspot +
                                                                                                      • How To: Working with Seurat
                                                                                                        • @@ -134,7 +140,7 @@
                                                                                                        • - +
                                                                                                          • @@ -160,7 +166,7 @@

                                                                                                          Checks the version of the Vision object and displays error if necessary

                                                                                                          Checks the version of the Vision object and displays error if necessary

                                                                                                          - 
                                                                                                          versionCheck(object)
                                                                                                          + 
                                                                                                          versionCheck(object)

                                                                                                          Arguments

                                                                                                          @@ -183,11 +189,11 @@

                                                                                                          Contents

                                                                                                          -

                                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach.

                                                                                                          +

                                                                                                          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                                                                                                          -

                                                                                                          Site built with pkgdown 1.5.1.

                                                                                                          +

                                                                                                          Site built with pkgdown 1.6.1.

                                                                                                          diff --git a/docs/reference/viewResults.html b/docs/reference/viewResults.html index 26e5ce1a..b0efee08 100644 --- a/docs/reference/viewResults.html +++ b/docs/reference/viewResults.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 @@ -90,7 +90,7 @@
                                                                                                          • - +
                                                                                                            • @@ -116,6 +116,12 @@
                                                                                                          • Incorporating a Trajectory Model
                                                                                                            • +
                                                                                                          • + PhyloVision and Hotspot +
                                                                                                            • +
                                                                                                          • + Spatial Data and Hotspot +
                                                                                                          • How To: Working with Seurat
                                                                                                            • @@ -134,7 +140,7 @@
                                                                                                            • - +
                                                                                                              • @@ -161,10 +167,10 @@

                                                                                                              View results of analysis

                                                                                                              # S4 method for Vision
-viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
+viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
 
 # S4 method for character
-viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
                                                                                                              +viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)

                                                                                                              Arguments

                                                                                                          @@ -199,17 +205,18 @@

                                                                                                          Value

                                                                                                          None

                                                                                                          Examples

                                                                                                          - 
                                                                                                          if (FALSE) {
+    
                                                                                                          if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-saveRDS(vis, 'vision_results.rds') # (Optional) Save results
+saveRDS(vis, 'vision_results.rds') # (Optional) Save results
 
-vis <- viewResults(vis) # Launches dynamic output report
-}
                                                                                                          
+vis <- viewResults(vis) # Launches dynamic output report
+}
+
                                                                                                          -
                                                                                                          +
                                                                                                          -
                                                                                                          -
                                                                                                          +
                                                                                                          +
                                                                                                          @@ -177,7 +175,7 @@
                                                                                                          -
                                                                                                          +
                                                                                                          @@ -282,7 +280,7 @@
                                                                                                          -
                                                                                                          +
                                                                                                          @@ -294,7 +292,7 @@